You can see why they did it. This is a girl group, so they're going to act out what they sing as they sing it. That means that if the object of their affections is a girl, they're going to have to dance around with and seduce a girl. Their fans don't want to see that, and their fans' parents probably especially don't want them to see that. But this is the whole problem: it's a move almost solely necessitated by homophobia. Yes, it does change the song's narrative in not-insubstantial ways for it to become about young lesbian lovers, but it certainly doesn't ruin anything, and the small bravery of the gesture in today's context could only be an enhancement. It's especially troubling when they have to go to such effort to make the switch: it's more than putting a "he" where there was once a "she," in this case.
The whole thing has always felt gross to me, whether in covers or in person: I've known, and you probably know, people who do the same thing to a song as they sing along with it. The thought of kissing or liking a member of their own gender is so offensive to them that they can't even allow it to pass through their mind in the most innocuous possible ways.
I've always wondered how people deal with The Magnetic Fields for these reasons. They have a number of songs ("I Thought You Were My Boyfriend," "I wish I Had an Evil Twin," "Acoustic Guitar" just off the top of my head) where the narrator/protagonist is clearly gay. This makes sense: band leader Stephin Merritt is gay. When you've got a song where the characters are ostensibly straight there's at least an argument to be made that covers switching the characters' genders are hewing to the spirit of the narrative, you couldn't begin to say that in cases like these.
Not a world-shaking issue, but one of those weird little places where people reveal themselves in a way I don't think they're entirely aware of.