Personally, considering how much of MOS echoes of the unmade Superman movies of the '90s, such as Abrams' version; and considering how many superhero-franchise third movies lately have been going for the "Rocky III" trope of 'The Too-Confident Hero Gets Knocked Off His Rocker In Some Way And Has To Find Himself Again', I would not be at all surprised to see WB go back to that Well Of Unmade Superman Movie Ideas again and use the Death & Return arc as the basis for the third MOS movie (this counting the upcoming Leaning On The Batcrutch as the second one), at which point I suspect Kara would be brought in.
That said, I can easily imagine a tie-in to the prequel comic and another echo of the Byrne era (specifically how Matrix Supergirl was introduced), where Kara is found frozen in the Arctic after having escaped the wrecked scout ship. Where I'd twist things, though, is have her turn her back on Superman once she learns he killed off the one Kryptonian who had dedicated himself to restoring their dead world - and that the Codex which might have been able to do the same is inside Kal-El's body where it's pretty much useless in its present form - and thus leave poor Big Blue to face Doomsday on his own with the expected results. Throughout the rest of the movie, though, she would begin to see that Superman has really left an impact on the people of Earth, as much through their deeds in the aftermath of Doomsday's rampage as through their wardrobe choices (she sees the S-symbol everywhere, not just on memorial armbands but graffitied on walls and even on T-shirts) and realizes that, primitive though they are, these Earthlings might not be a complete loss after all. And once it becomes clear that Brainiac's the one that set Doomsday loose to kill Superman in the first place so that techno-organic Coluan could get his nasty mitts on Kal-El's body and thus the Codex, Kara realizes somebody's gonna have to stop him, not taking into account that she's going to end up being outmatched, or that the aforementioned Codex will serve as the convenient deus ex machina by which Superman will end up being resurrected by the last third of the picture (after spending the middle third in the afterlife being convinced by Jor-El, Jonathan, AND Zod that he's got to find a way back to the living realm).
"My folks came to the U.S. as immigrants, aliens, and became citizens. I was born in Boston, a citizen, went to Hollywood and became an alien."