Mechanics of Game won't allow you to do that, you can only capture, I believe you can only capture enemy or netural but not anything your allies own (I could be wrong). And if you could, the only way your allies can take over your ships is to make them invalunerable and Can be capture, for that code, you might want to look at the netural asteroids ability...

...hmmm. There's an interesting idea. How to rig it would be mildly tricky, but... hn.

Set Trade Ports (It's as thematically appropriate as any) to have a Grab Ships ability that targets only allied craft. Then... hmm. Perhaps if you had a civilian vessel that you sent with your fleet, and hit the button to render a fleet 'capturable'... if there's some way to query whether a buff is already present, then it could capture only ships with said buff.

Call the ship an Ambassador craft or something and you'd be on a winner.

The challenge there would be whether or not you can have an ability apply only to craft with a specific buff present; if not the principle would work but be uncontrollable. Last thing you want is an ally nicking stuff you didn't want them to take... 

Well these are all very good ideas . I hope I can do this with my limited skills so far.