I wish I didn't have to do this, but unfortunately it seems there's no way around the conditional crashes the Homunculus can cause, just because of how the game handles damage on the enemy side. I've tried everything I can, but unless a solution presents itself (which it might), you can fix your save by doing the following:

Start by downloading the save editor - https://github.com/robojumper/DarkestDungeonSaveEditor

You click the "release 0.0.65" button to download the correct version. Get the .zip, not the source code. Unzip and run the .jar file, then set your save directory; if you play on Steam it'll be
C:\Program Files (x86)\Steam\userdata(your profile number)\262060\remote(profile)

Your profile number will be a string of numbers; there should only be one folder in the userdata directory unless you have multiple Steam accounts on your computer. The profiles run from profile_0 (top slot) to profile_8 (bottom slot), so make sure to load the one that actually corresponds to the correct save. Go to the "persist.game.json" tab, and look for something along the lines of
"inraid" : true,
"raiddungeon" : "weald",

where "raiddungeon" will be the dungeon you're in. Change it to:
"inraid" : false,
"raiddungeon" : "none",

to set yourself back to the Hamlet and fix broken saves.

If this doesn't work, I can't really help with the save editor since it's not my tool. You might be able to find a solution by visiting the Discord server linked in the mod description.