I think that Boomer is part of the plan, but the Cylon plan isn't total annhilation (if they wanted the entire human race extinct, they wouldn't be saving humans as breeding stock).
Boomer had another chance to kill Adama, and instead thwarted it, and she was wired directly into the Galactica's computers, and instead of crippling it, she destroyed a Cylon fleet.
The Cylons are manipulating humanity, pushing them, goading them. They've had their chance to finish off Galactica or key human figures more than once. Cylon priorities regarding Galactica seem to have changed after they found Kobol (but I think Galactica-Boomer's assassination directives had already been activated, and it's shown they aren't in constant contact, and she was driven nearly crazy already by the evidence she really was a Cylon when she was on the Base Star).
I think the Cylon "Master Plan" is for at least some humans to survive, and fulfill the prophecy (and the Cylons have placed a very high priority on biological reproduction, which has to involve humans because of limitations the Cylons have), and to find Earth. The Cylons claim they know more about human religion and history than the Colonials, and they have a monotheistic belief system (that in some places is outright Abrahamic).
The exodus from Kobol was only 3000 years ago, which means that Earth can't have been settled by settlers from Kobol (like was implied in the original series). Instead, I think the show is actually in the far future, after Earth is abandoned for Kobol many centuries/millennia in the future, then Kobol is left for 12 colonies, but one group of humans returns to Earth, and retains older human belief systems instead of a polytheistic belief system deifying rulers of Kobol.
Thus, the Cylons, with their strong religious beliefs, want the Human prophecy to come true (with the caravan across the stars et al.) so they'll find Earth and be converted to a monotheistic belief system (and the Cylons will find people who share at least a form of their faith).
Thus when Caprica-Boomer became pregnant, and Galactica found Kobol and the way to Earth it became clear that for the Cylon plan to work, Galactica has to survive. They have to make it look like they are hunting Galactica, and keep them on the run, but in the end it's more like they are following them instead of chasing them.
