I was just reading through old Dwarf Talk transcripts (like ya do) and I had a suggestion for the adventuring party autonomy question that was being kicked around a while ago. It seems like if you're just coming to a town to rest or restock or what-have-you it shouldn't be a concern if your party wanders off or stays with you according to their personality, but there should be a system in place if you're going to that town for a reason and don't want people running off.
There should be an option to shout to everyone around you a motivational speech referencing a specific plan of action, and basically put your social skills and language skills up against the personalities of your companions that determine morale failures or abandonment. So you go into conversation, shout to everyone, and go "motivate the troops" or something, and then say "we're going to kill Urist VampireBoots" and then the party around you sort of weighs that against their allegiances and their personality. Or it could be "we're going to go drinking" or "we can start a village here" And then instead of making it really complicated maybe just have a list of a few things you could promise people in regards to that. So you say a thing and your continuing dialogue options are "promise people riches". "promise people power", "promise people freedom" or security, or honor, or revenge or things like that. And if somebody is allied to Urist VampireBoots but is really greedy maybe the promise of treasure wins them over, but if you're trying to get people to kill a bunch of monks that took a vow of poverty and you promise them treasure they become more skeptical and might leave, so you can't just do all the options in a row and win everyone over. Maybe you do a speech, and promise everyone treasure, and one of your party still doesn't care but you go in individually and say "We're going to kill Urist, and I promise you freedom" and maybe that resonates with a person if their town is run by Urist or something.
And this would weigh against morale failures, so you finally get to the top of the necromancer tower or whatever and you've lost a couple of companions, everybody is weary and treasure doesn't sound that great weighed against lives. So you can motivate people only so far based on their personalities, and really skittish people won't stay in terrifying situations unless they're even more scared of you. Then you've got things like "we're going to kill Urist" and "I promise I'll punish you if you don't" or "We have an obligation to dead comrade #2, he was the bravest of all" kind of thing or even "returning alone is dangerous" so if only one person is threatening to flee they're considering if maybe it'd be safer staying with the other people with swords than risking a missed zombie or a guard patrol change on their way out. Or you just get to town and you're like "We're killing Urist for honor" and you just retreated from a battle somewhere else, the morale failure is just everyone abandons you to go to the tavern and you can't win that party back until they've drunk off the negative emotional cache from the last battle.
Of course, with the new personality rewrite this should be a lot easier. If you're getting some kind of recognizable negative emotions tromping through an evil swamp, you know you need to get your troops rallied at the end, but if it's just a trip across town from the tavern nobody has enough built-up negatives to have to worry about it unless the destination in town is really scary.