Sounds like they really are trying to help, and it's positive they are putting an action plan in place. I know it might seem like an overaction but they will have a behaviour management policy in place, and will be following this which they are required to do. I know at my sons nursery they had a zero tolerance policy for violent behaviour and would definitely have taken action if it wasn't an isolated incident.
As you say, I'm sure he will learn over time as he's only 3, but the nursery is doing the right thing by him, and the other children, by what they are doing right now. Best of luck x