My DH and I were also married-but-apart from March until October the 1st year we were married. I used the time to get all organized and apply for the visa, it didn't impact it at all (except in saving me some money because I could wait and didn't need to expedite the visa). Start gathering the documents, and then I believe you can have them post-date the visa up to three months (so you could apply in June and have the visa dated Sept?), so she can get up and go as soon as possible!
Good luck, others with better advice will be along soon!