From a gameplay perspective, it's useful to have controllable NPC's during the Nautiloid-tutorial so the game can explain how party mechanics work.
That said, it wouldn't be unreasonable for Lae'zel's equipment (armor at least) to be locked at least during the tutorial.
Then why control any companion later in game. I don't see the reason they would obey my orders. ;-)
Obviously we need a pokemon-like mechanic, where each companion has a chance of not listening to your orders unless you have high enough
gym badges approval.