I can agree that the suicide respawn time can be annoying at times, but it is in place for a good reason. The first being if a player commits suicide to spawn at the opposing base, obviously they should incur a time penalty. Committing suicide to spawn at the other base though is obviously highly discouraged as we would much prefer you to drive there in a hog yourself. The other as you said occurs when a gunner shoots at a target that is too close to the hog. The gunners obviously have the advantage over unarmed lone hogs, and so a gunner who suicides should receive a time penalty during respawn as the other team deserves to respawn ahead of that player.
As for CTF that is a betrayal timer. It makes sense that if you kill your teammates you should be penalized next time you spawn. Even if you didn't mean it, it is a good deterrent from betraying and gives an incentive to players to be good teammates and look out for each other.
