It was Holmes' decision
It was not because of the Golden Raspberry
Holmes begged off working on the sequel, she says, to pursue other projects, and was replaced in the role of Assistant District Attorney Rachel Dawes by Maggie Gyllenhaal. But that doesn't mean Holmes has any regrets about turning down the project, she insisted.
"Not at all. I had a great experience working with Chris Nolan [and] I'm sure it's going to be a great movie. [But] I chose to do this movie ['Mad Money'], and I'm really proud of it," she told MTV News.
(source)
So from Holmes' herself, we are told that it was entirely her decision to leave the franchise to work on something else.
Christopher Nolan has also said he wanted her back, but she wasn't available:
But Nolan revealed in the lead-up to “The Dark Night” that he had wanted Holmes to return.
“Katie wasn’t available for the role, which I wasn’t very happy about, but these things happen, and I was very, very fortunate that Maggie [Gyllenhaal] was able to take it over,” he said.
Gyllenhaal even personally reached out to Holmes to get her approval to take on the role.
(source)
This is also worth reading:
http://www.alloy.com/entertainment/the-dark-knight-director-disappointed-katie-holmes-turned-down-role/#ixzz4S4eIu5rI