I think they should make jokes about it. “You look different, did you change your hair?”
I say, just roll with it like nothing's different. Although, if they must, have Beth (Alice) save her and reconstruct her face like she did for Hush.
Remember in DC there are multiple universes & just like in Crisis Superman from different universes were different faces/people, so that's all we need to do for the new season, remember they never mention Kate leaving to help on the other planet earth anyway,so there it is, a different Kate on a different Earth