Pretty much just difference of opinion on conflict acquisition (easily house-ruled)?

I feel like the actions listed in the book to earn Conflict are universal enough. The issue lies in GMs who house-rule based on their own prejudices, or a fear of said GMs lying in wait out there.

My problem with the Morality system is simply this: it's not a mechanic for novices on either side of the screen. It heavily favors proper roleplaying and narrative structure, and when you introduce players and GMs who aren't used to incorporating those elements (or don't care to) it becomes what everyone fears. With a party of murderhobos, it serves to barely mitigate their bloodlust and opens the floor to pointless rules lawyering about which precise actions they commit will earn them how much Conflict.

Because of this, I feel like any "fix" shouldn't be applied to the system but to the table. When incorporating Morality, a conversation should happen at Session Zero, or at the very least before Session One. It should be part of the social contract from the very beginning. The GM should say outright that she's planning on running Morality as written in the book, or else provide a solid outline of her new ruling from the get-go. This shouldn't be a vote but a discussion.

And if it doesn't fit with the group and the GM thinks they can't handle it? Just fall back on the original rules as outlined in EotE or AoR. They still work with FaD, and while they do even less to curb the murderhobos, at least there's no perceived ambiguity. You take Strain to use the dark side, and the judgment of your actions as good or evil comes from the people of the galaxy rather than the Force itself.

I think just making it clear at the start how you plan to handle it will eliminate 99% of the problems. If the remaining 1% are philosophical deliberations on who is or isn't innocent when it comes to killing someone, then not only is the Morality system not broken but your game is probably making your players better people. Ultimately, however, it's important to remember that this isn't a vote. The GM's word is law.