I'm not sure how a program would take that (being told they are #2). I don't think it would make them hate you or anything, but it's not the same as telling them they are #1.
I think a better way (if you are able) would be to try and get some faculty member @your school to phone the PD @ your #1 choice and find out whether they are likely to take you there. Technically, they cannot say, but usually can say whether you will be ranked highly vs. not. If you find out that your #1 program isn't that highly interested in you (argh!) then it might be better to lobby program #2 a bit harder, including having a faculty member(s) call them in support of your candidacy. If program #1 sounds really interested, so much the better...and you can do something similar with them to seal the deal.
I think in cases of residency/fellowship placement, the PD receiving a telephone call from someone he/she knows, or if not that then at least someone who wrote an LOR for you, can sway them more than an applicant saying "You're in my top 3" or "You're in my top 2!". They hear such statements all the time and I'm not sure how much it really sways them. It's not what YOU say...it's what other people say about YOU.