In my experience (not direct, I did not serve as an elder), they may be lenient with someone who is forthright and explains their situation to them before they are discovered and confronted. Your wife would still have some sort of sanction applied, but it may not rise to the level of a DF. Then again, if she was committing fornication for a period of years before marrying a non-JW, they may feel that they have to DF her as an example.
The impression I get is that she understands that this may happen and is hoping that she can get back in the org's good graces with an eye towards convincing you to join her. I think her long-term goal is for both of you to be PIMI JWs. But if you're happy together and the only friction is from what the organization will do, it might be the wakeup call she needs, at long last.