I agree. I took that episode to be the journey of them discovering themselves. There are 3 parts to that episode: the initial shock and confusion, the denial, and finally the acceptance.
After the fake breakup Tweek accepts his feelings by telling Craig he made him "feel like he's never felt" which is the turning point. Afterwards, it shows Craig in his room looking sad since he probably shares the same thought but was too afraid to say it. Then his Dad tells him that he has come to terms with it and Craig can't fight being gay. Then we see them getting back together, for real.
I think the writers were definitely telling a deeper story than initially appears, and it perfectly captured the range of feelings. It was just a perfect episode overall, and sends a really positive message, especially to young people watching. I love how everyone is so happy for them and the other kids don't bully them. If only it was always so wholesome and simple.