I'd say "like" is not quite right here - we don't say "like the way", we say "in the way". And your phrasing at the end is wordier than it needs to be, you can use this really brief and (I think) quite elegant phrasing:
She doesn't see me as a close friend in the way that I do her.
Having said that, why not replace "in the way that" simply with "as":
She doesn't see me as a close friend as I do her.
It looks a bit weird written down, but in speech it's good.