The "You're not" expression can be interpreted any number of ways:

--trying to hide dismay that perhaps Rose is knocked up by someone else
--pleased at the thought of Rose having anybody's baby because he thinks she'll be a great mum, and perhaps it'll help heal her heartbreak
--longing to see their baby

It's a very ambiguous expression. You can argue it any which way. If they ever were intimate, I'm sure it crossed his mind that it could be his.