Now the reason I chose the target anyway was not because of the ship. I use Cobras for M7Ms and I have two of them already. I want this ship because it has a jump beacon on board. I couldn't care less about the ship itself in comparison. I just want that beacon. After that I don't care if the ship despawns.
Now, the boarding operation for the most part went off without a hitch. It was in a pretty empty sector, Cloudbase SW, and there were no other military vessels around. It being an M7M it was as easy as letting it burn through all its missiles until it became a sitting duck. The only issue was at the very end. I will use pictures to illustrate:

"Transferring ship control"

So far so good.

...what?
Ok, no problem. Just reload and do it again...
Same thing.
*Blink*

Goodbye Minotaur, jump beacon, and the 20 five star marines which have taken a week to train. I condemn your souls to the digital void...