You have two options, as others have said.
1) You can try to convince her to go along with the application, there's nothing that would force her to come to Canada. Even if you don't think you will reconcile, there is always the possibility, and if you remove her from your application, that option is dead.
2) If you are both 100% certain is over, what legal options are available to you? Can the marriage be annulled? If you have to go through a lengthy divorce proceeding, even just demonstrating that one of you has applied for divorce should be sufficient. Then add a letter like Veronica suggested.