Oh dear. Well of course pumping should not hurt, anymore than breast-feeding should hurt. However sometimes it does. It could be an issue with your pump, but it could also be there is just so much going on with that one breast that everything is going to hurt right now. It sounds as if you have overproduction on that one side. This definitely happens. I had this really bad with my third baby, and pumping was so unbearably painful that even though nursing hurt like the dickens nursing was better.
Hand expression might be the only thing that you can do that is comfortable. If so I would strongly suggest hand expressing. You want to try to avoid more pain and injury on that nipple as much as possible.
In my case it took very careful latch and positioning and nursing very very frequent before I was able to get things to calm down enough that nursing was comfortable. We're talking a few weeks of pain. I also had mastitis thrown in there to plus a giant plug it was a drag.
Anyway, if you would like tips on making pumping more comfortable or anything else let us know I just don't know what else you have tried. Personally I did have to see a lactation consultant to get help with my babies latch when I had these problems. But aside from that it just took perseverance to get through it. Within a few weeks I was able to nurse entirely comfortably.