Why Rogue Will Stay With The X-Men After X-Men '97 Is Over.

Because, despite what we are currently seeing in the series with her, to paraphrase what IGN said about Wolverine and Storm, "She's too popular of a character to turn against the X-Men."

So, no matter what happens in Season 2 and beyond, Rouge will still be with the X-Men when it's all said and done.