An official recommendation from the applicant's pre-medical advisory committee is required. In the event that such documentation is not provided by the applicant's school, two letters of recommendation may be provided from instructors in the prerequisite science courses
There's really nothing to be left to interpretation. They're saying that if your school has a pre-health committee service, you have to use it.
Your school's committee should have LOR requirements that are in line with med school requirements (i.e. they should require at least 2 science letters in order to cover the bases set by med schools). Mine required 3 science letters, one of which could be research, and 2 more letters that could be science, non-science, or character references.
If you're worried about them seeing the lack of 2nd science letter, give the school an anonymous call and just ask if the 2 letters are still required with the committee letter. Not sure why people are so afraid of doing that.