On the face of it, the guy might seem like a bit of a twit, but Eden haven't apologised on the basis that he was upset but on the basis that they do actually have a problem with the number of ants in there.
The biomes are not perfect replicas of the natural habitats and this seems to me to be a situation where the fact that they are unable to replicate all the natural checks and balances has led to one particular factor achieving a dominance it wouldn't reach in the wild.
I was at Eden in July and there certainly weren't ants all over the biomes then. In fact, I don't recall particularly noticing them at all.