Get some financial / legal advice and find out if there is some advantage to your wife in choosing separation versus divorce. In my experience there is often a financial reason.
I don't know how it is in your state but in mine separation was going to be just as costly as divorce, and then you'd have to pay AGAIN for divorce. Might as well go straight to the divorce.
Don't get me wrong - I'm not saying she won't wake up and snap out of it, she might. But if she's moved out and in an affair with another guy, and wants to file something, let it be divorce instead. Stop being her Plan B. Sometimes it takes them really knowing we have moved on before they can start to feel what they are losing. Take a look at PsySara's thread in Newcomers for an example of a spouse who turned around at the last minute.
Also, just because you divorce doesn't mean you couldn't reconcile in the future The divorce is about protecting yourself financially.