NJ Realty transfer tax - Title transfer to my LLC

[Peter J.]

I own a property in my personal name and I am looking to transfer it to my LLC.
I have a mortgage on that house.

My attorney prepared the deed for the title transfer and I went to the Clerk office of Morris County, NJ to record the deed.
The deed is a bargain and sale deed and the consideration amount on the deed is $1.00

To my shock, the county clerk's office does not want to record the deed because of the mortgage on the house. 
They want me to pay the realty transfer fee on the remaining balance of the mortgage.

We are talking several thousand of dollars. That is insane.
I am transferring the title to my LLC for asset protection and there is no other unrelated third party involved.

I don't think I should be paying realty transfer fee. It is unfair.
What should I do?

Have you been in that situation?
Any suggestion is welcome.

Thank you.