Is he overjumping to such an extremity that you cannot ride him? I know plenty of jumpers, who do 3ft and higher, who over jump small fences but put them up to a higher fence and they don't over jump. Honestly my pony over jumps anything under 3'3" at a show and under 2'3" at home and I've never really had an issue with it, as a result we never have any rails. If you cannot safely jump him then by all means don't do it, I'm just a little confused because I've never really known anyone with an issue with it. I'd only have an issue if my horse was jumping like this:
But if you feel unsafe then I wouldn't jump him.