Its not stealing when the game world keeps turning a blind eye to it most of the time. Think of it as appropriating resources needed for the investigation.
We are not in Kansas. Meaning, not worth fretting about much. If you dont want to dont, otherwise do.

Charisma is most useful for RPS dialogue battles so if you want to focus on combat the most you dont need it. I still didnt do a completely charisma, non combat abilities focused run. who knows what Larians hid there... (lots of quest and situations do have a non-combat option)

Nasty deeds are mostly worthless.

Arent stealth and invisibility branches on the same tree? Or rather, fruits on the same branch? Sweet delicious fruits. yum.

Best advice i can give: dont try to min-max the perfect single playthrough.
Game is meant to be played multiple times, solo and co-op.

Experiment, let the dice roll, live wild. (of course you wont, meh)