I didn't get what the concern here. If you are truly married then what's the worry. People who are married some time live separately for some genuine reason . Just tell them what the reason is.

Even if they deny it saying its fake marriage , you can easily fight it in court. When your wife personally testify in front of judge saying she is married to you and living separately for the period of time for this reason, they can't proof its fake. You will eventually get it.

If it's really a fake shortcut , then you should be worried , and also shouldn't get green-card. And if immigration officer will deny your application and might initiate deportation. Against which you will have no tool to fight with.