Since the last Mummy movie she won an Oscar, so she may be wanting to further her career rather then go back to a franchise she left around 5 years ago.
It is also a different director on board, and the rumours could be right that she didn't like the script.
Personally, I think it is a wise move on her part, she has 'The Lovely Bones' coming up which is directed by Peter Jackson, so I believe returning to the popcorn action franchise would be a step backwards.
While it's certainly a serious blow to the film, sources say all is not lost ... yet. Brendan Fraser and Jet Li are still signed on to star, and Cohen will indeed helm. Seeing as the third film will reportedly revolve heavily around the trouble-seeking son of Rick and Evy, perhaps losing Rachel Weisz isn't such a big deal after all.
I think she left because of - Tomb of the Dragon Emperor claiming that she felt uncomfortable being away from her son for five months to shoot in China or script issues.