You can't come up with some kid-friendly bullshit? "Creampuff got scared, like you get scared sometimes, so we're going to spray the room with good juju from this spray bottle and say the room is a happy place with each spray, so both you and Creampuff will know not to get scared again." And then don't have the kid handle Creampuff alone.

I tried stuff like that, like "creampuff promised to be nice and he wants to be buddies again" but my son wasn't having it. He was terrified and wouldn't leave his room, he has never been in the situation where something that he loved hurt him and now he thinks creampuff is going to hurt him again.

Also, things like mites can make a guinea pig suddenly start biting,

Where would he get mites? He's only ever been outside of our tiny and very clean apartment before we got him and as we were bringing him home.

and being shut in the dark is scary so even a healthy guinea pig would be jumpy and nippy afterward.

That I understand.

Guinea pigs aren't violent animals so your kid probably hurt Creampuff for him to suddenly react hard enough to draw blood for the first time in his entire life.

I was right there. He had him in his lap and was softly petting him and singing a song to him.

At age two, he might be too young to be trusted to interact nicely with small animals. ETA - Or, Creampuff could have mites, be injured, or ill.

I mean he was interacting nicely and did not seem injured, I don't know where mites could've come from.

I had a nippy dog as a small child (she was partly nippy because of being around small children, and at one point, because she was hurting from cancer), but my parents didn't get rid of the dog or shut her away. They told us to stop doing things that would piss her off/eventually got a super friendly, sweet dog to make sure nippy dog wouldn't scare us out of liking dogs.

By nippy do you mean that it would bite you?

If the dog was drawing blood and your parents didn't remove it then...