I am a little unsure about what you are suggesting here. Are you suggesting only free if a transport has military in them on unalerted planets, and current behavior (whatever it is) on alerted planets?
I was mostly suggesting current behavior on alert planets, never free on unalerted planets. Having just checked in a quick test game though, it certainly feels like most of the stuff that shoots at a transport already ends up free, so that suggestion may not be very different (if at all) from always free on alert planets, never on unalert. Not quite sure what I was thinking about the military stuff
- I thought military ships in transports could put a planet on alert, I'm not seeing that in my quick test though - 98 mk 1 fighters in a transport didn't alert systems it was in (but did when the transport died). Freeing based on military vs non-military would be rather clunky, and while I think I was worried about possible problems if it didn't free for military ships in transports I really can't think of any issues that would avoid, so ignore that part.
As far as it depending on whether the system is on alert, you just sent something non-cloaked into their system that they can see and consider a threat and are shooting at. Chances are it's on alert now as long as your crap is still there flying around, at least if there's enough of it.
If you're just sending transports it doesn't look like that alerts planets, unless I just wasn't sending enough transports in my tests. I'm pretty sure it treats transports like it treats scouts it can see, shooting at them but not really caring that they're there for alert status.
Edit: Except that currently it frees stuff that shoots at transports, but usually not for shooting at scouts, so it may be a bit more complex than that for alert status as well.