I did basic sci research in engineering and used that PI, but I see no reason why a clinical research PI would not be acceptable. HMS, like pretty much every other (research) med school, supports clinical research as much as it does basic, as far as I can tell.
When you're applying, the LOR requirements are a little scary, or at least they were for me and some of my friends. They sound very strict and specific. After going through the process, I find that only douchebag schools are super super picky about the LOR's, and I personally did not have any (confirmed?) bad experiences with LOR's. Use your clinical research PI and you will be fine--bonus points if you've worked with them for a while (likely) or if they've taught you a class.