Good question. I think Colbert and his character are too iconic to continue the show, personally. Maybe they'll come up with a different political show to replace the Report? At least that's what I hope, I just don't see a replacement being able to fill Colbert's shoes. As Meriadoc brought up, I think Colbert's character is key to this move. Will Colbert ditch the character, tone it down, or keep it completely on the show? Personally I see him toning it down. Colbert is smart enough to know his appeal lies in his character, but also knows the conservative character is a limited shtick that won't translate well to a more generalized late night show.
I have heard a number if interviews with Colbert, the man not the character, and he's brilliant and entertaining. I don't think he needs his character at all in order to take on this show. In fact, I think it would be a mistake to pigeon hole himself in that role moving forward. Moreover, I think it would be a mistake to not have someone else take over The Repor(t) on Comedy Central. There are other entertainers that could do something cool with that premise too. His character is based on Bill O'reilly, imagine someone doing a parody of Sean Hannity or better yet Glenn Beck! -that's my guess for the way this will all play out.