Thank you all for your kind words and advice, it helped me sleep a lot better that night.
It's resolved now but there was a bit of back and forth. What complicated things is that a few hours prior to me trying to place the deposit, I had emailed a form to transfer my booking to my travel agent.
The next morning I received an email from Princess saying that because my fare had been paid in full they couldn't transfer the booking to my travel agent (oddly enough they didn't respond to the second email I had sent them that night when the call centre was closed telling them I hadn't meant to pay the whole thing).
The first person I spoke to over the phone said that I would have to wait a week until my payment was processed for them to refund me the difference and then suggested that I keep the booking and ask my travel agent to book me a brand new booking with the travel agent, and then cancel the original booking once I had put a deposit on the second one. This didn't make sense to the travel agent because I would then lose the room I had wanted.
My travel agent suggested that I call Princess, cancel the cruise and asked to be refunded and then within the same phone call book the same cruise, same cabin and ask to put the deposit only with the person on the phone.
This Princess employee was fantastic. She didn't blink an eye at that and was happy to do it. She also said she would bring this up at one of their next staff meetings because it's very common for people to think they are just putting a deposit but Princess charges them the whole fare. She said there is a small button that I would have had to click but it's very common for people to not see it.
Anyway it's been resolved, waiting for my credit card to process the refund but I was forewarned that may take a week or so.
Thanks everyone for your help!