It depends on whether you are using a pre-med committee letter or not. According to my pre-med adviser, med schools will take whatever comes in the committee letter and not fuss about what kind of letters are included. I don't have any science letters with my committee letter for the reasons you mentioned - I would rather have 3 glowing letters with my committee packet than a positive, but generic science letter.
Just in case there were some schools who really wanted to see something from a science professor despite the committee letter, I got a science letter that I am sending through Interfolio apart from the committee letter. I expect it to be positive, but not glowing. I would suggest doing something similar. I don't know how well it will work, but my pre-med adviser thought it was a great idea...