I agree with Shangalar that if you're completely new to the game, you don't really belong in a Zone Control action. If you insist on going, then you should respect what your team mates are telling you. If you end up getting team killed in such a situation, there's often a reason for it, even if you may not agree with it or even know about it at the time.
Now there may be cases where people get teamkilled without reasons or for bad ones, but from a development point of view, this is a tremendously difficult problem to solve. How to define when somebody "deserves" to get killed and when he doesn't? The extreme points are equally unacceptable. Disabling friendly fire or extremely severe punishments for team kills is a bad idea, because then there's no way to stop griefers, looters and other people who are not contributing but only ruining the experience for others. On the other extreme, having no repercussions at all for team killing would also be bad because some people would just go around massacring everybody. So we're looking for something inbetween.
Having played a lot of PvP myself, I know how annoying it can be when you are interrupted in the middle of a fight by some bluesuits or noobs who have no idea what is going on. If there is no way for players to remove them from the battlefield, the consequences in terms of the fight can be rather severe. And few things can be as annoying as having a huge battle, barely coming out of it alive, and then comes 5 bluesuits from nowhere and run away with the spoils. I can't think of an obvious or easy to implement way to handle such thievery, so I think being allowed to shoot them is the best solution right now. This is why there are no reputation penalties during and just after ZC for shooting players who didn't contribute in the fight (players with less than 50 score from that fight).
From a roleplay and realistic perspective it's not exactly optimal to have team killing as a measure to prevent such things, but then again, death is also not permanent, so there's that. We've spent a lot of time discussing these issues but we haven't been able to come up with anything better as of yet.
Anyway, team killing in most cases is not tolerated, but during Zone Control the rules are lighter, and there's a reason for that. I'm open to suggestions for how to improve the system though, and the idea of a sort of "faction voting" against some player might be viable, though it would require certain measures to avoid mass alting and bullying as well.