Well, I saw the new issue of Weapon X and I am feeling a little better about this whole 'Jono-goes-to-Weapon-X' thing. From the way the X-Men just left him to the authorities it almost seems like they're trying to get a man on the inside of the Weapon X program, not just leaving Jono to his fate. After all, we didn't see the fight where the X-Men subdued Jono, and I hardly think the X-Men would leave behind a teammate who is in obvious emotional distress (well, a certain Rogue-bitch might...). I guess the whole set up was too neat. If they wanted Jono to be a real 'tratior' I would have thought that they would have made his defection a little less obvious, or at least wait until the second issue of the story arch to do the reveal.
In all honesty, I just think that it would be totally out of character, no matter how depressed he is, for Jono to join Weapon X - a very shady program that every X-Man knows about.