Your thinking wasn't wrong, the problem was that the municipal and provincial police and governments abdicated their duties and abandoned their citizens. The federal government stepped in because the lower levels of government refused to do their duty for weeks. I don't disagree that Trudeau stepped a foot beyond his jurisdiction, but in that scenario, he was being the only responsible adult who actively cared about the well-being of Canadians.
I'm glad it was done, and there was nothing in the execution that was heavy-handed or otherwise untoward. The people had more than ample warning to disperse, the line moved slowly (giving the people every opportunity to leave of their own volition), force was restrained and minimal. People got arrested because at that point they made the choice to be. It certainly was not the situation we currently see unfolding in the US right now (which, if we are honest, the convoyers would have wanted for their side to perpetuate, if they could).
WestJet only reversing it because word started to get around and people were swearing never to fly WestJet again. If there were no possible alternatives for flyers, they would not have cared.