An extremely silly question, buut...

[Batman]

Geo, the abandon ship order has some merit I think.

You are right that it would be a cheese tactic to be able to reboard the ships at will, but you could make it so that derelict ships have zero supply and a random number of (randomly determined) damaged components.

The abandon ship order could go in the Retrofit/Modify/Scrap order window. The damage-algorithm could be the same one as for damaging warp points.

You could maybe even add a mineral cost to reclaiming derelict ships. This would make it unattractive to abandon ships that you wanted to later reclaim, and give the abandoned ships a real "derelict" feel.