Well, wet areas are never good and can cause mold and eventual rot, but if you need a/c in the short term, what else to do? As far as the operation of the a/c itself, no problem.
One possible quick fix: with the inside cover off and looking up inside, you should see a bolt in each corner. This is a clamp, basically squeezing the upper and lower sections together over a gasket on the roof. One or more may have loosed up, so try tightening a bit. Not till to can't turn them any more, just more snug. It may solve the problem.
2004 American Tradition; 2013 Buick Verano
Homebase in the Ocala Nat'l Forest near Ocala, FL