Hi J.- I know your heart is aching in this situation. I had to put down two of my cats in the past year. One of them was barfing regularly and sometimes urinating, I'd taken him to the doc twice, he'd been on antibiotics twice and frankly, I was just broke, going through fertility treatments and couldn't deal with it anymore, nor could I afford to keep spending money on vet visits. Although it was a very hard decision to make, he was 13. So I said to myself, this is a quality of life issue, I'd given him many good years with a happy home. At age 12 a cat will start declining in health anyway. So I made the difficult decision and I although it was SO hard and sad, I knew that he'd died peacefully, without suffering and that I loved him.
Afterword I went to petloss.com for people grieving their pets and found that many other people had to put their pets down much younger for various reasons. Wanting to have a clean and healthy home is not wrong. I cried for a while, but then, when I didn't have to come home to urine and barf I felt better. His brother was left behind and he did miss him for a couple weeks, was looking for him, etc. But I just gave him lots of love and attention and he was fine. This year I had to put that cat down because he became diabetic - was 13 - and was urinating around the house. I wasn't going to be giving him shots every day and there was no guarantee it would work anyway. That was also very hard, and I still miss him, but honestly, my stress level has gone down a lot from not having to deal with the peeing on the carpet, the smell, the germiness of it, etc.
I think you should put this cat down. A cat of 12 years old is a senior cat. And you've been wonderful to him, but I would definitely draw the line when I have a toddler and the cat is peeing on his pillow and other places. Don't feel guilty. The pain will subside and you'll just remember what a great pet he was.
L.