How long did you have it in primary? I rarely secondary, leave mine in primary for about 3 weeks, then keg, being very careful not to suck any trub with the beer. Then I let it cold crash and carb for about a week. I get one or two cloudy beers, but far from a yeast milkshake. Even when I empty the keg and clean, there probably isn't more than a couple of tablespoons of yeast gunk on the bottom of the keg. As I said though, I'm pretty focused on not letting the autosiphon touch the trub.