Sorry to be the bearer of bad tidings, but this is the official word from TV Guide's Ask Ausiello:
Question: Please tell us why Sarah Wayne Callies isn't returning to Prison Break. We fans have the right to know. The Michael-Sara relationship is the only reason I watch.— Lisa
Ausiello: Well, you probably shouldn't waste your time petitioning the network to bring her back, since reliable sources tell me that it was her decision not to return to the show following her maternity leave. As I said last week, I'll have much more to say on this whole matter in the coming weeks. In related news, Callies' spokesperson confirms that the actress gave birth to a baby girl, Keala, in July.
from TV Guide: http://www.tvguide.com/ask-ausiello
