Personally, I don't think it is that big of a deal. The sippy cups we put them on require almost the same type of sucking as the bottle. My Doctor is very strict about this as well, she says on a sippy by a year. I battled my son for 3 months to get him to take a full feeding from one and wish now I wouldn't have chosen that battle. My daughter is 14 months and still takes a bottle at night and I am not concerned at all.
However, if you want to do this(which is perfectly fine by the way) I would remove the bottle and let him fuss for the first couple of nights. It might not take him long to figure it out.
I do not think anything is wrong with switching to a sippy cup..noone be offended please. I just don't believe it to be
as big of a thing as the doctor makes it sound....did your doctor tell you why?