If the GC or school feel that strongly about the rule, that is certainly possible. After all, on the school report ( https://commonapp.my.salesforce.com/sfc/p/#d0000000eEna/a/0V000001Avzq/PBXzR0UOtu4hSdgTXHDH9Sk6bTeQ6w8l2NQblq_KoZ0 ), the counselor could check the “discuss this applicant over the phone” box (and then mention over the phone the applicant not obeying the school’s rules) and change the overall recommendation from (presumed) “enthusiastically” to “with reservations”.
If the school’s policy is to avoid top students from “crowding out” other students at other colleges, then sabotaging the OP’s application at the other college s/he wants to apply to will fulfill this goal of the school as well.
I do not agree with the policy either, but I would not be surprised if a school that had that policy for that reason would “enforce” it in this manner, which they are well within their power to do.