I wouldn't over-complicate things too much.
Just make that certain items owned by companions won't be "interactable" unless you kill them or far later in the game until a certain rate of approval is reached.
Locking equipment slots is one thing, and even though I didn't really like a similar approach in DA 2, I can understand that.
However, when I start with a non-STR class, locking me out of the only mule's inventory in Prologue is a bit too much. A big bit.
