Sona was on the panamaniam prison (so prisona or something?) Basically they were saying: we've lost, but we can contain them by having them not return and get one locked in prison. If it's Micheal, Linc doesn't have quite the know-how to get him out. Just a theory.
I think he figured she was too power hungry to do that; considering he knows she had her brother "killed" and framed a guy just so she could get power, he probably felt this wasn't something she was at all likely to do. I'd favor a big twist in Season 3: they get out of the country, and they...
We've seen him before, with him writing the notes instead of talking. He's the president who supposedly died to let the Veep woman take over the office. We thought the poison did him in. Apparently not.
Ok. I hadn't watched a single episode of Prison Break until last week. I have now, over 6 days, watched all of Season 1 and caught up in s2. This is a great show. Sometimes a little far fetched, but I'm really digging how things go in this. :)