Did your doctor do an ECC? If so, what was the result? If not, insist on it. If you truly have cervical abnormalities without HPV, I can definitely understand why the doctor would need a live specimen. But if there is no dysplasia in the endocervical canal, a cone biopsy seems awfully extreme. The least he could do is dilate you to have a look to see if there is something higher up that needs to be addressed, immediately.
I do, however, think you need to get a second opinion and possibly have the biopsy/ECC redone. A different doctor may see something the current doctor doesn't.
In addition, which HPV test did he do? If he did Digene, it's limited in what it detects, and you may have a strain it doesn't read. However, if you truly do not have HPV, is he planning to run other tests to make sure you don't have other reproductive organs involved? I'm just thinking of all the possibilities you could have your doctor check.