Recently DS is fascinated by the skins of fruits and eats them too (even he gags on the skins most of the time). I am also worried about that.
Nowadays, I always wash fruits with Environne and then rub them against a brush under running water before offering them to DS, hoping that this can remove the surface pesticide, but I don't know how much it remains inside the skin.
Peeling the skin can eliminate the risk (also suggested by our government's centre for food safety), however this also means much of the fiber is gone.
Buying organic fruits may be the way out, but they are very very expensive here. Sigh.