Like everyone said above, I wouldn't sweat what you said. He asked, so he broke the rules first. What are you supposed to say, "No I'm not gonna rank your program number one, please move me down your rank list and let me have no shot of matching here." However, since you do like his program, I would still let them know at the end of interview season that you "intend to rank his program highly." I think everyone who's been doing this long enough, knows that that means you're gonna rank them probably top five, and there's the chance that you will end up there if they want you, but not guranteed. If you're still worried that even doing that is gonna hurt you, then just keep your mouth shut and let things work themselves out. I think it's kinda petty for a program to drop you down their rank list because you don't rank them number one, but who knows how some PDs think. My opinion though is that you should let your top programs know that you are interested. However, as previously mentioned, don't tell everyone that they're number one, otherwise you could end up screwing yourself in the future.
