So? Bigger, truly loved characters have been killed off in TV series before (e.g., ER's Mark Greene, a number of characters on The Walking Dead), and the shows moved forward. Some minor number of shippers don't keep shows afloat, and no one should listen to them. There's no risk. A handfull of people might whine. No biggie, as the showrunners are not strangers to screwing over characters (yes, I mean James Olsen).. How? Supergirl's ratings have always been low, and surely you can sense that the show is winding down. You had one longtime series regular leave this season, and I would not be shocked to see another depart sooner or later. That, and Benoist probably has a desire to do other things, not stay in that costume for another two or three years.