I have to say it never crossed my mind as being gross. both times I didn't want them to take my lil one away even for a second to see if it wasa boy or girl! with DD1 I knew I was a mother the instant I looked down ab hour after birth and didnt even care my hand was covered with pooh!!! the other thing is I LOVE the newborn smell, but my sister said 'she smells funny' when she held DD2. fair enough I suppose considering what she was covered in, but I think its just another one of those natural mother-newborn bonding tools God gives us!
That said, if you find it a bit gross when it happens, just ask for a towel for bub