Kara moving to the future was a fitting end to her story arc, promising the character happiness and a boyfriend --and tidies up the DC universe for the powers-that-be.
The ending made sense for that rendition of Kara, who's not -quite- from Krypton and didn't have -quite- the same cousin tie to Superman. The big problem I had with that episode was that it was rushed, so the romance was super-forced. With a cast the size of the Legion, it should've been a two-parter, like the other time travel episodes showing new bunches of characters were. If the Fatal Five wasn't "bad" enough, have Mordru be behind the scenes.
I think part of the point was establishing parity between the Justice League and the Legion Of Doom (by any other name), so they get rid of some big guns from the JL side (Supergirl, Martian Manhunter), while still keeping them available if need be.