Now, if you were the Jovians, what would you do with a Minmatar battleship that has been upgraded with Jovian tech? I can't think of anything that Clear Skies could do in Jovian space that a Jovian ship couldn't do better. In fact, there is only one advantage that Clear Skies has over Jovian ships: it can run around non-Jovian space without drawing much notice. On top of that, the ship's crew have shown themselves to be competent and reliable, once they've been convinced to do a given job.
The obvious answer, then, is to send them back into the rest of the universe as your agents, perhaps after upgrading Clear Skies further to give it a major edge against any subcapital it fights. Heck, it might even make sense for Smith to use Clear Skies as his command ship.
The Jovians in Clear Skies 3 made it clear that they were worried about their tech falling into the wrong hands; according to EVE Online's lore, capsuleer technology was one of the Jovians' gifts to the various empires. It's entirely possible that in the universe we see in Clear Skies, the various empires had to do without, and just came up with more efficient automation systems; that's how a Tempest can be flown by three people, but they need to be walking and moving on the decks of the ship instead of sitting in a gel-filled pod. (That plus the need to have characters actually visible and identifiable for drama purposes, plus scrapping the capsule-cloning mechanic which leads in-game to Death Is a Slap on the Wrist.)
The selection of Rourke and company (but especially Rourke) for highly dangerous missions, his strict adherence to ethical action even at great risk, his reluctance to use violence despite repeated opportunities, his strong need to justify (often outloud, directly to his aggressor) his decision to kill, and his long standing and profoundly affecting regrets over its misuse - in my mind, this would make an ideal candidate for attempting to reintroduce carefully measured aggression back into the Jovian population. This also helps explain Sascha's abrupt romantic overtures, or even her presence: she's Smith's catspaw; she never said she wasn't a Jovian agent just like him. The only evidence we're given of her allegience is when she jumped in on the side of the Gallente to counter John's assumed pro-Caldari stance; she probably only did that to make him admit outloud that he had a neutral stance - which is essential for a Jovian agent. Notice neither Sol (23 years Caldari Navy) nor Charlie (ex Gallente Presidential Guard) jump to their respective race's defense when Sascha goes pro-Gallente during the planning session in CS 2.