I am not aware of any rule that requires the diagnosis to be made microscopically. In other words, although it is not common (and maybe not an accepted) medical practice, I don't think it breaks any coding rules. (If there are any, I'm open to hearing them.)
That still doesn't mean I would advise it, for a couple of reasons: One is that if records are requested, the payer could challenge the CPT code, and, without the path report, there will be no proof that it warranted a malignant code. Second is that, if the doctor does this regularly, could lead to suspicion that he is fraudulently treating stuff that doesn't need to be treated.