I hope this situation will be corrected in the next update so that one kill doesn't lead to this result.

Yes, and that is actually my overall point, the penalty currently is way to severe, especially considering the FIA faction is supposed to lay ambushes, traps, mines, etc.
A good solution, if possible, in my mind would be to ensure a single kill is not enough to go straight to Renegade and that friendly fire on mines for the FIA only counts as friendly fire if within a certain radius of a FIA base.

That is weird.
Was you able to actually see the different FIA bases? For me everything was yellow markers (unknown) and when another player tried to add me to he's squad it said I belong to another Faction (most likely also why I couldn't even get the option to unload the supplies in the pause between the FIA ai Boots where shooting at me)

Yes, when you have normal rank, experience is clearly displayed for unloading supplies, however, the problem was that a single, fully unintended incident gives you Renegade rank and when having Renegade rank, supplies cant be delivered, because you are no longer part of the faction.
Just tested this to confirm it, eventhough it was quite difficult to do, since all the ai FIA trops now shoots at you :-)