I agree Therrien probably disliked him. His actual comments about Subban were condescending and arrogant as hell. But Bergevin? I don't see it. There's no day-to-day relationship between GM and player. They don't work directly together or have regular contact. Even during contract talks 90% of discussions are with the agent. Today's GMs are much more insulated from players than in the 70s; I can't see them making trades based on personal feelings.
The people most closely affected by a player's personality are teammates. Teammates work alongside each other every day and spend the most time with each other away from the job. Teammates will be the ones who develop likes and dislikes for each other. I can see a locker room of typical low-key jocks getting annoyed by someone so much louder and in-your-face than the rest of them. Doesn't mean you still can't be friendly and high-five someone who annoys you (The counter-arguments are a little silly, to be honest: "Look - Markov kissed him! They like each other!", "Look - Price low-fived him! They're friends!"). It just means being annoyed isn't a 24/7 state; plus, NHL players are hyper-aware of what not to say in public.
Like I said, none of this makes Subban a bad guy. It simply suggests his tone grated on his more stoic teammates (this is, after all, the roster that voted Mr. Stoic for captain). Subban was a huge presence in Montreal. Bergevin knew the move would be hated but did it anyway, most likely to appease, in order, 1) an unhappy locker room and 2) a dumb coach. Ultimately, Bergevin made a hockey move, but only as a response to a group-dynamic problem.