Yeah, they stink. I hear ya.

I run a pipe cleaner thru the stem and swab out the bowl with the same cleaner but they still stink a while.
I store just-smoked pipes outside in a well ventilated area (garage, pole barn, shop) for a few days before moving them back inside. I also find that keeping them inside some kind of a wooden cabinet with doors that close helps to mitigate the stench. I imagine one of those cheap 100ct humidors would work perfect if you wanted to get fancy.