Etymonline offers no insight. The British National Corpus has three cites from 1989, 1991, and 1992. The Corpus of Historical American English has two cites, from 1981 and 1986. Wiktionary doesn't say anything about etymology, but marks the phrase as UK, Australian, and has a much older cite from Rose Of Spadgers by C. J. Dennis, 1924. The most extensive discussion I have found so far is over at The Phrase Finder:
There have been a few attempts to explain the origin of this odd phrase. [...] The more prosaic suggestion — that it alludes to the practise of throwing stones at crows — is much more likely.
I've found mid-20th century references from England that describe it as an Americanism and American newspaper articles that call it 'an old English phrase'. The dates of those are more or less right but not the locations — the phrase appears to have originated in Australia. Most of the early citations in print come from down under. It has a sort of Australian twang to it and is in common with several other similar phrases, all with the same meaning: starve the bardies [bardies are grubs], stiffen the crows, spare the crow.
Partridge also lists "starve the bardies or lizards or mopokes or wombats", marking them all as Australian expletives, and noting that "Wombats may also be speeded".
Christine Ammer, The Facts on File Dictionary of Clichés, second edition (2006) has this brief entry for smoking gun:
smoking gun Definite evidence of illegal or criminal activity. The term alludes to smoke emitted by a revolver or other kind of gun that has been fired, but it is also used more broadly for other kinds o malfeasance. For example, Time (Sept. 19, 1977) had it, "In fact there may be no 'smoking gun'—no incontrovertible black-and-white evidence of wrongdoing by [Bert] Lance." The New York Times (Oct. 4, 2004) quoted National Security Adviser Condoleeza Rice, talking on CNN about aluminum tubes in Iraq suspected to be used for nuclear weapons, "We don't want the smoking gun to be a mushroom cloud."
The use of "smoking gun" as a literal description of a gun with smoke rising from its muzzle goes back to at least 1843. From Alexander Marlinsky, Ammalát Bek, serialized in Blackwood's Edinburgh Magazine (June 1843):
"What mark can be better than the breast of a foe?" answered Ammalát Bek, riding up, and at ten paces' distance pulling the trigger! .... the gun went off: and slowly, without a groan the colonel sank out of his saddle. His affrighted horse, with expanded nostrils and streaming mane, smelt at his rider, in whose hands the reins that had so lately guided him began to stiffen : and the steed of Ammalát stopped abruptly before the corpse, setting his legs straight before him. Ammalát leaped from his horse, and, resting his arms on his yet smoking gun, looked for several moments steadfastly in the face of the murdered man; as if endeavouring to prove to himself that he feared not that fixed gaze, those fast-dimming eyes—that fast-freezing blood.
The first Google Books match for "smoking gun" in a figurative sense comes from this rather amusing anecdote told (by an unidentified speaker) in American College Health Association, Proceedings of the Annual Meeting (1966) [combined snippets]:
We must prepare in advance our course of action and try to avoid what can be called a "smoking gun decision." The story that describes this type of decision involves a court trial of a man who claimed permanent injury following an accident in which he was struck by a car while riding his horse. In the course of the trial a state highway patrolman described the accident in which a speeding car ran full into the plaintiff on his horse as he rode across a rural highway. The patrolman stated that when he asked the plaintiff if he had received any injuries, the latter had replied, "Of course not! I'm feeling fine." The judge interrupted the proceedings and asked the plaintiff to explain this obvious disparity between history and current complaint. The plaintiff told the judge that as he sat on the highway near his severely injured horse the highway patrolman came up and, going over to the horse, shot him between the eyes. The officer then approached the plaintiff as he sat on the highway and, waving his smoking gun at him, said "And how do you feel?" He said, "Judge, under the circumstances I felt very well." Let's avoid "smoking gun decisions" in the next few years by adequate preparation and organization, recognizing the strength of our well established convictions, standards and principles.
As used by the speaker, a "smoking gun decision" is simply a decision made under extreme duress, as if while a smoking gun were being waved at you by the person asking you for your decision.
The first instance that Google Books finds of "smoking gun" in the sense of "irrefutable proof of guilt" appears in the context of the Watergate scandal of 1973–1974. The phrase "a smoking gun" or "the smoking gun" appears at least six times in Facts on File, Editorials on File, volume 5, part 2 (for the year 1974). And the earliest of these appears in an editorial from the [Cleveland, Ohio] Plain Dealer, (July 11, 1974):
At a minimum, they [transcripts of White House conversations] demonstrate an impeachable failure to uphold sworn constitutional duties. The White House naturally challenges this interpretation and complains about the manner of release, but, significantly, it does not challenge the fundamental accuracy of committee transcripts.
True, the evidence so far does not show the president with a "smoking gun in his hand"—the phrase used these days by congressmen who would prefer an ironclad case before doing anything. However, to pursue the analogy, it is undeniable that a large number of dead bodies keep showing up at Nixon's feet. The cumulative result is highly incriminating—and no amount of dodging and diversion by White House lawyers and apologists can obscure that cold fact.
I wouldn't be at all surprised to learn that lawyers in the United States (and elsewhere) have been using "smoking gun" in the figurative sense of "decisive proof" since long before Watergate. But the Google Books database yields no smoking-gun evidence of any such usage from before 1974.
Best Answer
@DavePhD's excellent answer reviews the provenance of the phrase at issue. His research suggests that it is a known English phrase that is overwhelmingly used in reference to a paranormal event from New England in the 17th century. The conclusion would appear to be that it is not (or at least was not for a long time) a slur towards Muslims or anyone else.
However, as any student of language knows, context matters. Perhaps, the context in which this phrase is appearing (a Magic the Gathering card from a set called Arabian Nights which was released in 1993) is enough to elevate an otherwise innocuous phrase to the level of ethnic slur. Indeed, it begs the question: What would possess someone designing an Arabia-themed card game to reference a little-known event from 17th century New England? Many people have suggested that the name is actually a derogatory reference to Palestinian "stone throwers" especially given the timing of the set, which was nearly contemporaneous to the First Intifada. Even barring an intentional allusion, the slight towards Palestinians might reasonably be inferred from the context (i.e the Arabian Nights set) since Palestinians generally consider themselves Arab.
These poor optics might be enough to err on the side of caution for a company whose product is under scrutiny; however, I believe that there is further missing context which makes good sense of this card without reference to any pejorative. Specifically, in Arab mythology, djinn are widely understood to throw stones as a way to pester (and sometimes kill) passersby.
This open-access edition of One Thousand and One Nights contains an historical note about djinn, including this observation:
The translator here is referencing this quote from his own 1835 book Modern Egyptians:
This source (which itself is quoting Majmoo’ Fataawa al-Shaykh Ibn Uthaymeen (v. 1, p. 287-288)) attests to this history as well:
This website which aggregates paranormal activities in Arabic countries claims to report a news story describing djinn throwing stones in Morocco in 2010.
As an additional aside, there are also instances in which djinn have stones thrown at them (presumably as a dramatic reversal of roles). The open-access translation of One Thousand and One Nights linked above includes the observation that some Arabs have believed that shooting stars are stones thrown from heaven to kill evil djinn. This could potentially parallel the Stoning of the Devil (an allusion to the djinni Iblis) referenced in the original question. Also, one of the first stories in One Thousand and One Nights is "The Story of the Merchant and the Jinnee" which begins with a man throwing the pit of a date (called a stone) over his shoulder and accidentally killing a djinni's son.
Clearly, djinn are well-documented stone throwers. It seems apparent that the Magic card "Stone-throwing Devils" is referencing this. One might ask why "devils" is used instead of "djinn" since Magic the Gathering is no stranger to the word. I suspect that the designers were trying to reserve "djinn" (a rather uncommon word in English) for exceptional and rare creatures since only 4 "djinn" appear in Arabian Nights. The term "efreet" is also used a few times in the set - again in reference to rare creatures. With this goal in mind, using the word "devil" makes sense. "Devil" would also help to emphasize the obvious Biblical pun in the flavor text of the card.
Contextually translating "djinn" or "efreet" as "devil" or "demon" is not such a strange idea. This journal article argues in favor of using different English words to describe both the different levels of and different motivations of djinn. Both "devil" and "demon" are addressed specifically. This article admits that "djinn" has no direct English equivalent, so while transliterating the word might be acceptable, it doesn't seem beyond the pale to find a common English word that conveys the relevant meaning in context.
To summarize: "Stone-throwing devils" is not a slur as such, and historically, it has no immediate connection to Islam. However, when put into a modern Arabic context it can begin to carry some contextual baggage. In the specific context in which the phrase is used here (namely, an Arabia-inspired fantasy setting), it seems clear that that baggage has been misplaced.
EDIT: @TaliesinMerlin tracked down this article from 2002 in which the designer Richard Garfield explains the origin of this card's name:
This would suggest that the controversy has existed for a rather long time already. Additionally, the description he provides is in keeping with the stone-throwing djinn hypothesis proposed above. I have attempted to locate the story in question but have been unsuccessful. It is possibly a misremembered reference to Sinbad's Third Voyage in which giants kill Sinbad's crew by hurling stones at them.