Some animals will just never get along. If you absolutely can't get rid of one, you'll have to keep them separated.
Back home, Dad and I have three cats. We started noticing that my cat was suddenly having accidents, and we couldn't understand why...we thought mayhaps she was going senile, since she's really old. Then one day we saw her go to use the litterbox only to be scared away by one of the other cats. That cat was just playing, but my cat has just gotten too old to be able to play those games. Since she basically always stuck by me anyway, we confined her to my bedroom, and the problem got solved. Now that I don't live there anymore, she is still closed up in there, but Dad took down my bedroom door and replaced it with a screendoor so that my cat doesn't feel so cut off.
So...while it may come down to separation and one of them being confined, you can find creative ways to do it that aren't extremely inconvenient. Good luck!