Here's the update: Things around the office have generally gotten better. There are a few (three, to be exact) in the office of 18 that are still disgruntled about the whole thing. They rarely speak with either of us, and find ways to complain about us (she's too loud, I came in late, etc). My boss has become fairly understanding-- he even will ask one of us about how the other is doing. I was called out to a family emergency last week, and my boss regularly checked in with my partner about what was going on with me.
Our jobs are less on the line, but we find that the stigma has still taken down our percieved professionalism. I think of it as a detante.
As for the kids, they like me more and more. I'm like a favored uncle (and I love it). There are some awkward moments, like when her youngest wanted me to put her in bed instead of her father, but it's all working out ok so far. My partner is easing them into seeing some physical affection between us. She now will hold my hand in their presence or lean into me on the couch.
I find that the poly thing is easy for kids to grasp-- I personally think it is more natural to understand than monogomy. Where it gets confusing is when they are told monogomy is the 'best' or 'ultimate' form of relationship by others in society. When my partner's kids hit puberty, then it will get more complicated. That should be about two years, assuming we stay together.