I swim at our Y pool, and haven't experienced anything like this. I did once at an outdoor public pool. Most pools I've been associated with are very good about health regulations and keeping the pool safe. I would imagine at the Y they are very good about it. Generally, they clear and close the pool in the event of vomit or feces or other such things and clean and treat the water. There is so much chlorine in that water I don't think you all were in any danger unless you came into direct contact with it, although it's not a pleasant thought to be in a pool with poo! And I wouldn't be concerned about going back there - I'm sure they have addressed the problem, but you could call and ask if you are worried about it. I'm not sure what your employer is angry about - you weren't responsible for the poo and you got the kid(s) out when you noticed it. I would have reported it so they could get the other people out of the pool, but I'm sure somebody else noticed it and reported it eventually. What did they catch from the warm water pool? My kids and I spend a lot of time in pools and we have never caught anything from a pool except for swimmer's ear. I was confused by your post though, were you alone with your nanny kid, or did you have another 6YO with you that was your child? Not that it matters...
Life's a journey, not a destination.
It's easier to stay on plan than to get back on plan.