From what I've seen, that game-still-running issue isn't just a modded-Banished problem, it happens with a few other games now and then on Steam, and with unmodded Banished.

Speaking purely for Banished:
Whenever you make any change to your modlist, after you confirm the changes you should take the time to entirely exit Banished and restart it. It seems to be an extra step that's needed to really "fix" those changes in the game's settings/memory.
If you start a town without taking that extra step, the next time you try to quit the town to go back to the main menu you'll most likely crash. And when trying to quit the game totally from your town, you might also get a crash although those don't seem to always happen. If you're on the Steam version of Banished, I suppose that could be the reason for those fatal errors you're having.

OK - thank you!

I had this same issue. Thanks for addressing it. I did what you said and it worked. Started the game, enabled the mod, quite the game, restarted, and everything worked fine from there. No more fatal error when exiting the game.