In real world answer: Guys, I got it wrong, it should have been like this... Then just either retro-fit the deeds or just run with what happened.
In game world answer: Your character suddenly realises that something wrong happened. The whole thing should never have panned out the way it did. Something had messed with with reality. What happened? How did it happen? Maybe more importantly, why? Now, you as a GM, have just added another layer in the cake that is the game. The player will have an interesting thread to follow and build something on it.
Barring in mind that in Pathfinder, and D&D as a whole, Good and Evil are not just concepts, but measurable, detectable, fundamentally defined forces of the Universe; such acts will draw attention from extra-planar beings.
Setting aside what the player/character has said to other players/characters, ask the player what his character is truly thinking he is doing. Is it simply because they are evil, and that is how the world works? Is it because he just wants to kill, and evil creatures are justifiable targets in the grand scheme? Or does he actually feel that allowing them to exist will only cause destruction and mayhem, and any blood they spill will be on his hands, metaphysically speaking.
If the first, either explain to him that is not how it works and continuing to do so will have consequences, possibly both through alignment shift and in-game NPC interaction. One example would be shopkeepers and merchants refusing to do business with a cold-blooded killer or anyone they associate with, thus impacting the entire group. Maybe the local constabulary has a "reward" for the character that has to be claimed in person, that is actually a pair of manacles and a jail cell.
If the second, have a devil, or other Lawful Evil outsider, contact him when he is alone; either on watch or in dreams, est. Have them make promises of power and reward for not only continuing his actions, but convincing others to copy him. This provides the opportunity for role-playing an individual with real issues. If you are not comfortable with actually giving him anything, have it be hallucinations to further drive home the point that what he is doing is crazy.
If the third, have a Good aligned NPC or outsider make contact and explain that while they appreciate the intentions, and applaud the effort he is putting in, he may want to dial back the zealotry a tad, maybe include a story or proverb about a historical figure that underwent a similar campaign. Or, instead of requesting him change his intensity, have them ask to change his directed target. Gobins are bad, but nothing compared to the demon-summoning, undead creating, walking personification of Evil that is tyrannically ruling the kingdom to the [pick direction] and is gearing up for invasion of the party's current location.
In summation, talk to the player, and act accordingly to his response.
Best Answer
I think this shouldn't be a dilemma for you, the GM. It should be a dilemma for the players.
If a player can craft a super-secret Alchemy Stone which will single-handedly turn the tide of battle against the forces of evil, then they will want to craft it. However, if it takes two months of intensive work to create, then the forces of evil are still moving against them in the meantime. This causes an interesting issue for the players to solve in-game. Do they take the time to build the super-secret Alchemy Stone? Do the forces of evil know that they are attempting this and try to stop them? Perhaps that would be an interesting session idea; the one character is trying to craft the MacGuffin, while the others defend his efforts from the adversary.
If it's less plot-related or dramatic crafting (like just a decent potion or other "nice-to-haves" for the characters), then you can consider simply allowing the following understanding: every night before bed, the character spends an hour performing whatever their craft is. You don't have to play this out every time. Then, after an agreed upon number of in-game days, they get whatever their trinket is. Even this is somewhat of a stretch, though, since for most crafts it would take at least an hour just to set up their equipment properly.
With that said, this is the very reason that crafting skills generally don't mix very well with an adventuring party if you're attempting to be realistic about the time frames. That's why every fantasy video game simply glosses over the crafting with a blacksmithing sound ("clang-clang-clang") and perhaps a very short timer. The amount of effort it takes simply to smith a sword is enormous, never mind whatever complex things your PCs are likely attempting. So you can either compromise your realism slightly in order to maintain the fun of the game, or you can let it be an interesting in-game dilemma.
To address the specific issue mentioned in the comments below: If you want your Wizard to be able to scribe spells into his spellbook faster but don't want to directly manipulate the rules-as-written (RAW), let them go on a quest for a magic quill which allows faster scribing or something. This would be a (hopefully) interesting in-game solution to a problem that the characters face.
You seem to be looking for an out-of-game, sort of meta-game solution to what is ultimately an in-game problem. And it's in-game problems which make games interesting. No amount of meta-game shenanigans will change the fact that in the real world it takes a week to simply forge a sword, so you will need to either bend reality, change the rules, or trust your players to handle it. For me personally as a GM, I would never force my Wizard to spend an entire day putting a new spell in his spellbook, because it's my opinion that the RAW are not the most important thing. My job as a GM is to remove obstacles that are in the way of everyone having fun.