I don't think there's a way to solve that problem. At least in a way which doesn't feel redundant or convoluted.
For example being able to "lock" the seat makes no sense, because then it would be easier to just remove the 2nd seat and have the driver seat be the gunner as well. By doing that you also lose the ability to have 2 people cooperate on the gun, as rare as that is. In an ideal world every player should be smart enough and have the decency to figure out how to deal with AT guns. It's not even something you "learn" by playing the game. Just by looking at someone manning an AT gun you can deduce that it shouldn't be moved, because someone intentionally placed it there.