You mean the sump pit.
I have never heard of anyone "sanitizing" their ground water sump pit.
I lived in a house for 17 years with a sump pump and pit, and never flushed or sanitized it in any way. The water comming into the sump is ground water, and unless it is contaminated with sewage, I wouldn't worry about it.
If you have to, a quick flush with a mild bleach solution followed immeadiately with a clear water flush will not damage your sump pump.