What kind of a dish are you using?
I suspect that if you're getting an odor the dish may be of a slightly absorbent material, you're waiting way too long to wash it out, and/or you're not thoroughly cleaning the dish afterwards.
Wash the dish out immediately when you see something like this happen, for the safety of your snake. If the snake wants to drink, the snake is going to drink the water, regardless of what's in it. How would you like to drink water that's been soaking with your own feces?
When you wash the dish out out, use diluted bleach instead of just rinsing it out. Scrub it thoroughly and rise it a couple times and wipe it out before filling it with water and putting it back in the cage.
I sometimes use antibacterial wipes to clean but I prefer to use bleach and I know a lot of snake owners do too.
You may want to get a new water dish. If it's maintaining a smell, it's probably not fully clean and may never be. When/if you get a new one, I'd get a different kind--one that won't do this so you don't have to repeat this process.