My husband was also a faithful Muslim man until he declared he became an Atheist simultaneously when he walked away from our marriage. It's so odd that a good spouse who has followed their faith most of their life can suddenly flip a switch like that!
When I spoke with a lawyer and a called a mediator in January neither specified whether it's better to start the process sooner or later. Perhaps sooner is better if you've already reached the point where you can envision moving on and if a year has already passed since BD and there's been no real progress towards reconciling. I can also say that now for myself after six months has passed since the divorce announcement and we're neither reconciled nor divorced that staying in limbo isn't terribly great either.
I do hope your wife will wake up and save herself and realize what she's done. It'll be too bad if that happens after divorce, especially if you no longer want her back in the future. I wish there'd be some way to prevent these situations from happening. Most of us never expected this so how could we have known?