1. check GCMS notes, they will tell you exactly what happened until recently (if she has actually requested withdrawal or not). Status in your GCI account is not always accurate.
2. in any case if you are really in process of spousal separation leading to divorce, it would not be wise to use it, even if she did forget to inform CIC or did not do it a proper way. Doing so might put you in problems even later (your history will be trackable to her and if she will claim new common law overlapping period of your spousal sponsorship, there will be a problem).
3. Once that one is done (be the withdrawal process initiated from her side or from yours), you can apply using different stream (for example express entry if you have enough points).
Anyway this attempt to immigrate, because you were married so long and because it was spousal sponsorship, will have no impact on chances getting any future visas (you wanted to rejoin your legal spouse and not just to leave and immigrate in a different country). But of course you can count with more scrutiny on your any future immigration to Canada. But as long as you have nothing to hide, no problem there.
