This isn't a generic "nobody likes being autobalanced" whine. There's a few real problems that put the team getting the new player at a disadvantage: 1) The player they get is in a class where they've already invested money into skills. This is problematic if, say, you're that team's third Support. It would be best addressed by letting that player cash in their skills so they can change classes if they want and reinvest that money. 2) Same problem as above, but on class limit servers. If you're switched to a new class entirely, all the money you put into skills is wasted and impossible to retrieve. 3) Firebases. When you switch, your deployed firebase blows up, and you have to wait for it to recharge. Switching a support to the other team and forcing him to recharge one of the most agonizingly long skills in the game puts that team at a disadvantage.
This in particularly is an incredible joke if the server has highlander settings whereby only one of each class is allowed and due to uneven numbers, you've lost your assault or support. While not guaranteed this can put a team at an massive advantage because players can potentially become deniable assets where the money spent during the game has effectively been lost and thus become the weakest link in the team trying to rebuild a new set of skills to replace the previous player.
It is annoying. It should change you with your current class and skills. You should get to continue playing whatever you were, even if you break class limit. It should be the only way to break class limit, is if you autobalance because the other team had to be losing in the first place, right? Anywho, I would just leave the server if I were you. (not me in particular, I wouldn't mind playing any class really)