Hmm. I haven't been seeing this, myself - despite encountering the "fighter disabled mid-pass" situation multiple times, so I decided to run a quick test.
What I did is put a Piranha bomber on top of an Apogee, then deployed the Apogee's drones. The Piranha's engines were knocked out by the ion cannons, and it got pushed out of the Apogee's bounds while dealing damage. The total damage dealt to the Apogee was something like... 40? 50? And it was pushed out lengthwise, not sideways, so it was close to the worst possible.
Are you guys seeing this with vanilla ships, or only modded ones? The collision damage heavily depends on the relative masses of ships, so if a mod's ship masses are out of line with vanilla values, that could cause problems.
The other two possibilities are that I'm either not reproducing quite the correct scenario, though I just tried it a few more times, or that I'd fixed it between the last release and now, though I don't recall doing so.
(By the way, the way I did this was using Run Simulation in dev mode. You can tell the Apogee to hold fire, deploy the Piranha wing, unpause, press Ctrl-F to turn off fog of war, select the piranha wing in the command UI, press F4 twice to destroy two of the fighters (must be unpaused to work), press F3 to take over the lone surviving one, maneuver it over to the desired position over Apogee, take over the Apogee, and deploy the drones.)