There are some counties that require the people to appear in person and anytime something has to be sworn it must be done by the actual person and it can't be done using a POA.
My understanding in KY is that some counties require moth people to be there and some do not. I know that Louisville was still issuing licenses allowing prison weddings, as do Jefferson County, Lyon County and some others. The best thing to do is call some orher counties and see which ones will allow it.
In addition, the warden of the facility has to okay it as well, but you have to have the marriage license first.
Here is an article on the issue and where someone filed a lawsuit about this.
So, to be clear, it is legal for you to get a marriage license so long as they don't require him to be there or to get sworn. You can find another clerk's office that will issue the license, several clerks in KY still issue them you just have to find an office that does.
Also, if you have a lawyer there where you live they can likely call the clerk's office for you and get it handled.