This is a tough one for me, at first I was going to say YTA, then NAH, then ESH. I think I'm going to stick with ESH. For context, I'm allergic to peanuts at about the same level as Josh.
Why YTA: You need to eat them in a more private space if you really want to respect their right to safety. Amy may have said he's okay with "some peanut dust" but you really never know what might set off a reaction. Hell, one time I had a reaction to somebody touching me after they ate a PBJ, and I usually don't even get reactions from that. The body is strange like that. I really appreciate that you're trying to wipe down the counter after eating, but think about it this way: Imagine I come home after work or class to find out that just a little earlier my family was eating whole peanuts from a tub on the kitchen counter. I'd be afraid to eat or prepare food there 100%. I understand that whole peanuts can cause a lot of crumbs, but that's really a small price to pay for true safety around the house, and that would be a way to actually respect Amy's boyfriend's right to safety.
Some say I’m the asshole because he can’t help that he’s allergic to peanuts, and I’m creating an environment that may make him uncomfortable.
This is why they are saying it: It's one thing to eat peanuts when somebody is away, but it's another thing to keep them stored in a public space where he can see it. It may sound stupid, but it's psychological. I've sometimes opened the pantry at my parents' house to see Reese's cups and had thoughts racing through my head, even though it was very irrational.
Why Amy is the AH: Although I appreciate how hard Amy is trying early in this relationship of hers', if I had found out that my SO was talking to other people in a shared space about my allergy for me and making requests for me, I'd honestly be a bit livid. My allergy (and Josh's in this scenario) is life or death for me, so that's a request for ME to make. What you need to do is have a 1-on-1 conversation around him whenever he comes over about this damn tub of peanuts. Stop talking to Amy about it because her and your stubborn-ness will only cause further tension. He's the one with the allergy, so you should be the one to talk to him about it.
Hope this helps.