While introducing a new BF matter of factly seems like a good approach, I find it odd that an MC would not suggest that at TWO MONTHS into a relationship, introducing a child to a guy who might disappear next month is .... potentially hazardous to the child.
Frankly, this is a discussion for the pediatrician, not a MC, anyway. Your daughter's doctor is the one with your daughter's interest at heart.
I'm glad overnights are starting with you. THat's great progress. The notion that overnight at Daddy's is somehow traumatic, while having some strange dude overnight in the house (and trust me, no two-year-old is NOT going to figure out that the guy is sleeping in what was Daddy's place--let's not underestimate children here) is okay.
At least half of the equation has been balanced appropriately.
(I think your MC is wrong about this. I don't think s/he is the right person to consult regarding the potential effects on your child. I don't know that it's in any way enforceable, but perhaps if your wife heard from someone QUALIFIED to render an opinion, she would rethink this idiocy.)