I think that Naomi is honestly working for Penny, with nothing to do with Dharma or the Others. She probably communicated with Patchy simply because he was the one patching her up. (no pun intended) If I was on the edge of death, or had a serious injury, I'd communicate with that nearest possible person, and I'm pretty sure it was Mikhail when she became able to do any talking. I can't rewatch, so I'm not sure. That's just my two cents.