As described by the narrator at the start of Chapter 1, Emma's life is almost too perfect. She has barely gone through suffering at all.

What Mr Knightley sees is that sometimes a bit of suffering can make us a better person, and this is a very gentle sort of pain. He wants her to be humbler, but without injuring her in any material way - and as you say, it's not quite as harsh as unrequited love. Yes, being in love with doubt of a return hurts. But once she has learnt to overcome that, she might know how to not value herself so highly. In theory, anyway.