The hard part(s) about dealing with this situation? Maintaining the momentum for the whole group, and doing so without just totally handwaving the problem away. You need to strike a balance between a game having consequences, and a game being un-fun. I don't know what options you've got for running a short-lived solo campaign with the caught player, while the team outside does jobs? Or an email back-and-forth, sort of like a play by post, with that player, in the meantime? Stuff like that, maybe?
'Cause to me, that's the tricky part. You want to do cool things with the guy who's locked inside, but you don't want to do it at the expense of the rest of the game (and vice versa, you don't want him to sit on his butt for a whole evening of gaming, while everyone else has fun).
Now, if and when you can get a handle on the logistics and timing of this sort of thing? Yeah. In my opinion, the best way to handle it is to make the caught player suffer a little, but not cripple their character or lock 'em up without a key. You want the campaign to keep rolling, while you still want there to be some repercussions to getting caught. The trope-safe way to handle all that? Some variation of "mysterious implant" (it doesn't have to be a full-on bomb, but that's kind of the tradition!), and the cops using them. Using them actively, instead of letting them rot in a crate or just throwing them back onto the street.
So yup. It's time to work for free for a little bit. Take a rep hit, maybe. Have folks not really trust you. Do some nasty work that the cops don't want to do for themselves. Yeah, all that fun stuff.
