Star Trek

Did he go to a  Federation Prison

No, he was shot, drawn-and-quartered, keel-hauled, urinated on, and dropped in an active volcano. 

Probably has the cell right next to Leyton in the ex-Admirals wing.

He got on a plane which crash landed on an island.

Good question.  Can you trust your penal institutions to prevent such highly placed criminals (e.g., admirals) from ever escaping?

I had thought you might be able to exile them to an adversary's space.  But, then, they would possess enough knowledge about Starfleet to present a real threat.

Would it be acceptable to lobotomize such criminals, rather than execute them?

Hmmm, he definitely committed a serious crime in Federtaion terms but he was motivated by concern for the Federation.  Dropped in active volcano?  I would send Lore there before Pressman.  Also, I wonder if the pro-cloak faction would go away that easily and suspect that they may continue to operate with increased secrecy.  Also, let's consider the USS Defiant.  That ship - and its Romulan supplied cloak - was sometimes used "illegally" in space outside of the Gamma Quadrant.  So, sometimes it is okay to break the rules?  I'm guessing that some splinter group in Starfleet Intelligence secured Pressman's release and work continues to employ a phasing-cloak for the good of the Federation.  A UFP black ops, as it were...

Admiral Pressman probably did have friends in high places, so they could have secreted him away, to scheme another day.  He probably would have liked to "borrow" the cloak-equipped Defiant for a mission or two.

One word and a number: Section 31.

Of course!