I called CIC helpline to ask about this just a few days ago, we submitted our application in October. The agent on the phone told me that changing the last name after submitting the application would lengthen the processing time since they have to update everything, and it's better to do the name changes after PR is received. So either change her name before sending sponsorship application and update all of the documents with the new name, or wait until after a decision has been made on the PR.