[RPG] How to guide the players into realizing they have multiple options available for an encounter

You have several options here, all of which include changing the players' tactics and/or changing your own.

1. Enforce consequences for the PCs' murderous behavior
   If someone came into my castle and started murdering my cooks, I'd have my guards after them so fast they wouldn't see it coming! Just because it wasn't in the written records doesn't mean it didn't happen, especially if the written record is two thousand years old. The castle lord should respond reasonably to having a bunch of murderhobos running around his castle. Putting consequences to their actions should help encourage the players to be less aggressive about meeting new NPCs, which in turn should alleviate some of the problems with their "if I can knock it out it's a servant, if I can't it's a monster" mindset.

2. Give the party a reason to bring along an NPC
   Maybe the party's goal is blocked by an enchanted doorway that will only open for a specific person. Maybe they can't find their way around the castle and need a guide. Maybe they need a hostage to deal with the guards who are coming after them for attacking servants. Whatever the reason, make the players realize that they need one or more NPCs alive and cooperating with them.

3. Give your NPCs some teeth
   You mentioned you tried giving your NPCs some stats, but it's not clear from your question why this didn't work. Not all NPCs should be level-one minions, regardless of what your players want. Guards will have a few levels in some melee- or ranged-weapons class; people in robes are wizards or sorcerers on retainer; the nice woman in a simple dress is a humble but powerful cleric; the nobles are trained in the fighting and/or arcane arts as part of growing up rich. You should also check the various Monster Manuals for low-level commoners - usually these show up under keywords like "cultist" or "guard", but if you reskin them to wield butchers' knives instead of swords, or broomsticks instead of staves, you've got perfectly good servants whose lifetimes of backbreaking work mean they're tough and strong and perfectly willing to fight back when attacked. Once your players get used to the idea that not everyone who isn't a PC or an enemy is a one-HP minion, they'll stop jumping to conclusions based on perceived stats.

Basically, options 1, 2, and 3 are meant to show the players that their current salt-and-burn tactics will cause their mission to fail. They encourage the players to find solutions to problems that don't simply involve a sharp blow to the head. The fact that they also give you more room to use doppelgangers is a handy side effect.

4. Have the doppelganger play along to deflect suspicion
   The PCs knock out everyone they come across? Sure! The doppelganger plays along and pretends to be unconscious long enough to fool the party, then gets back up and goes about its business.

5. Get one of your players in on the doppelganger action
   I did this in my current game and it was beautiful: the PCs didn't think through the consequences of leaving a single guard alone in a hallway in a doppelganger lair, so I sent an IM to the player asking if he'd go along with his character being ambushed, knocked out, and replaced by a doppelganger. The player had a ton of fun playing the doppelganger pretending to be his character, and the rest of the group took considerably longer to clue in because the player was involved in the scheme.

Options 4 and 5 are more about the doppelganger behaving intelligently, plus my favorite DM advice: get the player in on it. The doppelganger wants its mission, whatever that may be (kill the PCs? stop them from completing their mission? something else?), to succeed, and will take reasonable actions to make that happen. Getting one of your players in on this also helps them feel more excited about the plot, and they may even come up with good ideas to fool the other players that you'd never have thought of.

A word of caution: Doppelgangers, by their very nature, will drastically increase the PCs' and the players' level of general suspicion and paranoia. No matter how careful and smart you are about including doppelgangers, you should expect and be prepared for the players to take their own, often drastic, countermeasures. My group, after their one doppelganger encounter, developed the peculiar habit of shooting each other with crossbows to prove they were really themselves.

This paranoia comes because it's frustrating to the players when they can't trust the "rules" of the game world. One doppelganger is problematic enough; when half the NPCs they meet are doppelgangers, the players are likely to lose trust in the DM and the plot (unless you provide a VERY compelling story reason for why there are so many doppelgangers around and impersonating random servants). Once this happens, they're likely to go back to killing everything on sight because they've been burned by doppelgangers a few too many times. I'd strongly recommend being judicious with your use of doppelgangers to minimize this.

Let me start off by saying that Curse of Strahd certainly has some very challenging encounters, many of which can be stumbled into at points when the party is woefully under-levelled. I've only run it once so far, but that did end in a TPK.

In Vallaki, the party has the opportunity to run into a nest of vampire spawn whilst investigating a coffin maker's shop. The coffin maker (at least under my interpretation) is being kept as an unwilling servant/hostage of these vampires. I tried to give as many hints as possible that the coffin maker was scared of something in the shop - he was glancing over his shoulder, refused to let them in, would only speak in a whisper and asked the party to meet him later 'somewhere safe' suggesting the inn. Unfortunately the party didn't take the hint. Instead, they separated, two distracted the coffin maker, whilst the remainder broke into his house. I tried to give further hints - letting them spot many footsteps around large body sized crates in the dust of the storage room. I even pointed out that the cleric in the party felt something deeply disturbing from the room. Irrespective, he cracked open the crates, triggered an enormous fight and ended up dying.

It's important to note, however, that this type of danger is a common feature of sandbox campaigns. On top of that, this is a horror campaign - it is not unreasonable that if the characters poke around the dark corners of Barovia whilst uninformed of what lies within, they may end up angering something much more powerful than themselves. I personally feel that without such a threat, the player paranoia and tension necessary to maintain an effective horror theme can end up being lost or diminished.

Players should be made aware of this when starting the campaign and they should note that often discretion will be the better part of valor. It also behooves the DM to provide more narrative warning in such cases - signs of danger, direct warnings from NPCs, and (for when it all goes awry) avenues of escape. Even with this, however, encounters can and should have the potential to be fatal. At that point it is down to each DM how such an encounter plays out - nothing precludes you from granting strokes of luck, fudging rolls, or throwing in timely ally arrivals when things go south. Only you know your players and the game you are running, hence it's up to you and what you most feel makes for a fun game around your table.

With regards to your specific examples:

Death House - this is a hard starting adventure, but one that I found to really set the scene and vibe of the campaign. The shadows at the statue, the two ghasts, and the shambling mound stand out as all potentially being fatal encounters. The shadows, however, are extremely avoidable and are essentially a consequence of a lack of caution. Much of their threat depends on the party composition and their ability to output magical damage. Contrary to the book I would probably not have the shadows pursue the party out of the room, and may have them vanish if (for example) the orb was returned. The ghasts and the mound are tough, but certainly doable if the characters play smart.

and

Bonegrinder - I feel that warnings discouraging the party from entering too early are key to this adventure. The Vistani at Tser Pool may have warned the party away from there, knowing their destination and based upon what is written on pg. 28. Additionally, the raven should be extremely vocal in trying to ward off the players. Remember, the raven will be in league with the wereravens of Vallaki and essentially a force of good. Hence, assuming the party did head in and end up in fight against the three hags, having the raven summon help in the form of a swarm or a wereraven may be one solution to avoiding a TPK.