Technically, if it's a feature then auto-designating team killers as enemy does make sense as a simple solution for modifying the friend-or-foe stance to evoke a proper response from friendly AIs. However, in cooperative modes (PvE) you have to also account for possibility of unintentional TK, as well as a matter of any existing bugs (1), such as the one where drivers/pilots get unfairly punished for their gunners' mistakes (2).
1 - http://feedback.arma3.com/view.php?id=20339
2 - http://feedback.arma3.com/view.php?id=11593
I might be wrong though. Maybe it all plays out as intended and none of these issues are even related to each other.