While I definitely think the mind stone had a massive effect on Loki in the first Avengers film he definitely wasn't under full control, in fact I don't even think that's how the mind stone really works, definitely not like Clint and Selvig were.
What I think happened was Thanos tortured the hell out of Loki, and here's a silly little gorey through for you, forced him to battle other beasts, and if he won, his prize would be dinner... He would be forced to eat his fallen opponent.
Anyway, this took a toll on Loki until he finally broke, and that's where Thanos stepped in with the mind stone.
See, Thanos is evil, but he's not stupid, and he knows that loyalty born from respect and admiration is stronger than that of fear, that's why people die for their loved ones as he's probably seen countess times while invading planets. So he took Loki's broken mind and twisted it, the torture, the pain, the suffering, removed everything, his entire memory of being tortured, but he kept the loyalty. He filled Loki's mind with peace, promises, and purpose because that's all Loki's ever wanted, to belong, all thanks to the glorious Thanos.
That's what the mind stone does, it grants you peace, and a purpose, it makes everything... quiet... it doesn't make you do things for the wielder, it makes you want to do things. That's why Loki never spoke up about his experiences, he doesn't know where the mind stone stops and he starts, and he doesn't remember the torture.
Whenever you disobey the influence you experience something like withdrawal, a deep sense of panic and fear, of loss, of losing yourself and your purpose. This was severely amplified with Loki as he already suffers from intrusive thoughts, hallucinations (when he's having a really bad episode) and having no sense of identity (especially after Thor 1).
Then years later on the ship after Ragnarok Bruce Banner gets the sneaking feeling that Loki wasn't behind the attack. He questions Loki, asks him things like "don't you remember throwing Clint off a building?" or "don't you remember when you held Natasha hostage?" things that never happened and Loki just agrees because it was all a blur to him. That's how Bruce finds out about Thanos sending Loki.
