Having been a ref for a number of years, and done more than my share of rec league games, here's my 2 cents.
I would have told your center to get out of the paint. If after I'd told him he stayed there, than yes, I would have called 3 seconds.
It's hard to judge as there are a lot of factors I don't know. How long was he in the paint, did the ref tell him to move, how old are the kids?