That's a very good point. Look at how well she handled learning that Dexter and The Ice Truck Killer were brothers.
And I don't think she will find out in the first few episodes, if it happens at all. Each season is about 12 or 13 episodes long. So if she finds out at all, it'll be gradual. She'll probably piece it together at episode #8 or so, then wrestle with her feelings about it for an episode or two, then confront Dexter about it in episode #10 or 11.
While I think she will eventually come to accept Dexter for what he is, it won't happen over night. She'll agree to keep his secret at the end of Season Five, then come to fully accept it (and possibly even throw some "work" his way) midway through Season Six.
My only question is, if Deb does discover Dexter's secret, how and why does she find out? My guess? Laguarta is still insisting that Doakes was not the Bay Harbour Butcher and asks Deb to investigate it, off the books, and try to figure out the truth. During the course of Deb's investigation, she discovers Dexter's secret and has to decide whether to turn in her brother and clear the name of an honest (if not totally by the book) cop, or maintane the "status quo" by keeping Dexter's secret.