I think the only way you will find out the answer to this question is to call/email the school, just like I will have to do about my additional letters to Pritzker. If I had to guess I would say that they will not "let this slide" just b/c you send it in without them telling you "no you can't do this". They will also be unlikely to appreciate the fact that you tried to pull one over on them. Moreover, most medical schools are going to require AT LEAST TWO letters from science professors so this is going to be a problem for you at many schools. If you are applying now you have likely taken physics, gen-chem, bio, and orgo, so schools will probably wonder why you can't get 2 letters. They will assume that you are "trying to avoid it" which may raise a red flag, regardless of whether or not the letters you have sent are "really good recs". Another problem that you will run into is that you can have this packet sent and the schools website will say "received". You will sit around thinking you are good to go waiting for the complete sign to pop up and it never will. By the time you realize something is up, you'll call, have them tell you that you haven't met their requirements, then have to go track down someone to write the LOR and get it sent and wait wait wait again. (This happened to me last year and when I finally called the school they said "Oh I see you have a Master's degree, so the requirements are different for you. I will note it and mark it complete.
) I'd get that science letter like yesterday if I were you. It'd be one thing if you were adding extra non-science letters but not meeting the requirement won't go unnoticed. Afterall, no one can speak better for your ability to perform in med-school than professors who have observed your academic abilities in science courses. I'm no adcom member, nor am I trying to rain on your parade, but I just don't think this they will let this slide.