I don't remember frigates having this much problem avoiding friendly fire. Tried Frontal shields and Omni, tried with Accelerated Shields and with Auxiliary Thrusters.. my tempests end up taking more damage from my flagship than they take from enemy fire. And thats both with autofire on or off. With it on, i barely fire my beams even though they might pass clear of the frigates, but it doesn't even hesitate to fire a Gauss round that will eventually end up impacting the engines of some poor friendly frigate. Manually firing, they still have a deathwish to enter my cone of fire.
I'm ending up actually separating myself from my frigates just so i won't damage them. Didn't the AI in previous versions try to avoid your 'mouse gaze' while targetting? And speaking of, i didn't see any ships do the heroic 'take one for the team'-behaviour to take a shot instead of letting it pass on the ship the player's piloting.
Put a character up to 40 flying a capship with frigates and this is really becoming a problem. The number of time a Tempest sets itself exactly in my line of fire and refuses to shove off even though it could attack with both weapons from another angle made me weary of using them in an assist role around my flagship.