I think you have to be careful to differentiate between pain and control. The pain may arise, especially in pinning techniques, but it is just a tool to keep control over the center of uke. But it is necessary - as a control whether nage applies the technique correctly. I may be wrong (started just a few months ago), but anyway..
Painful throws? A lot of experience for me, mostly with people who just want to show off and forget that I am just a beginner. And one special day, when sensei showed me that Yes, ikkyo can be very fast and effective in bringing uke down on the mat. He told me to relax completely before he did it - fortunately for my shoulder joint..