It’s heartbreaking because Blair admits she loves Chuck much more wildly & passionately than Louie, but doesn’t love his antics. Hence the “happiness isn’t everything” line. She wants to trust her partner, and they’ve lost that. Chuck comes to the realization that he‘s too much of a mess to be with Blair, even though it kills him to let her go. He didn’t think he had it in him to become the man she needed. Ironically by walking away, he’s forced to seek professional help and become that man, and that’s why this is the wrong goodbye.