Update:
Decided to just go to the clinic on Monday because we were getting nowhere with them on the phone. I brought printed pages off the CDC and USCIS websites and I highlighted all relevant parts, I even brought my laptop with me. When we got there I explained how we were told I needed 2 doses but the official guidelines and recommendations say I need 1, at which point I showed her all the papers I had. I asked if we could see the Civil Surgeon and she said he wasn't in at which point I mentioned that we were told on the phone that he would be in on Monday. I said we paid $300 and either we get our money back or we get the services we paid for done correctly, the woman at the front desk tried saying we already got services so there would be no money back. She wasn't having any of that until I mentioned filing a complaint with the State Medical Board. She took some of my papers and left.
After a small wait the CEO came and talked to us. I pulled out my laptop and walked him through everything starting from the USCIS website to the CDC website to the ACIP recommendation that go back to the CDC website where it finally says in clear letters: 1 dose. He had no counter argument and just said he will have to talk to his team and the Civil Surgeon that actually was there, the woman at the front desk had lied to us.
After an even longer wait the CEO came back and directed us to a room in which we waited until the Civil Surgeon joined us. He asked what the problem was as if he had no idea and I told him how I only need 1 shot instead of the 2 he asked for. The started saying how he knows the requirements and it's actually the ACIP who makes them and it's 2 doses. I pulled out my laptop in front of him and opened the ACIP recommendations website that clearly shows 1 dose for routine vaccinations and he refused to look at it. He just kept saying there's no need for me to show him and would not even look. He filled out my I693 and did not mark my MMR as complete but wrote "1 dose documented" which does nothing for me and was still incorrect. I forgot to write my A-number on the top of the pages and I asked if I could do that really quick, he left the room so I had time to write that and review the I693 form. When he came back I mentioned that he filled out the vaccination part wrong and asked to have the CEO present in the room with us. He quickly changed his tune, took the Vaccination portion of the form and left the room to redo it. He eventually came back with it done correctly. I reviewed everything to make sure there were no errors and then I handed it back to him to have it sealed. We got our sealed envelope and copies and went on our way.
An absolutely exhausting process. Sorry for the really long post, we are just glad to finally have this whole thing behind us.