Since it's not beta yet, let alone release, we can only throw ideas around to prevent possible griefing and intentional team killing that will inevitably come out of the free to play system, since everyone and their moms can create a new account for the sole purpose of making their enemies' life a living hell.
This is what popped into my head just now, that would keep intentional team-kills at a minimum (hopefully).
First: minimum level to qualify for the big league. Let's say that you would need a 5 level minimum in order to activate friendly fire (or whatever number the devs would see fit). Besides making griefers having to work for the privilege to annoy others, it would help new players to ease into the game, giving them a bit of leeway in the beginning. After every level, you would get a noticeable message (mailing system?) that would remind newbies that at level 5, s**t will get real, and the time necessary to reach said level would deter trolls from bothering with it, but still short enough to qualify as a learning period at the same time. I think I overstated it, but there, couldn't be clearer.
And second: a way to give actual penalty for intentional team kills. Sure, it will be unavoidable that someone at some point will accidentally shoot down a Galaxy full of friendlies, but I'm also sure, that there is a way to catch those who only register team kills over a certain period of time (or a disproportional large difference between friendly to non-friendly kills). Of course, notable griefers would have to be punished in a way, that would force them to wait a long time to be able to grief again (temporary ban in extreme cases, for which I thought this little system up in the first place) and they would have to make a new account in order to keep playing (unless they wait, what they won't).
I'm sure the developers threw ideas around way more than my little brainfart here, but I thought I would share, if by some cosmic coincident this option didn't come up yet.