The writers have said multiple times that the overarching theme of the show is that it’s about “the things love makes you do” — and that sometimes those things aren’t pretty.
We see that on multiple occasions, whether it’s the beautiful relationship in episode three, Joel taking Ellie because it was Tess’s dying wish, Ellie picking Joel to continue the journey even when Tommy was a more logical decision, Marlene ignoring the lie when Ellie’s mom died.
And then in the final episode we get Joel choosing to kill off the Fireflies to save Ellie and Ellie’s desire to turn her friend’s death into something meaningful. Love, it ain’t always pretty.
To argue Joel didn’t love Ellie is missing the creator’s point completely.
