That part in Three Worlds Collide is intended to show that future humanity is as far removed from us as the Baby-Eaters and the Superhappies are from future humanity. It's not put forward as an example to follow. Shock and disgust are the intended reaction. (Also as a sidenote, I remember Yudkowsky saying that he probably should have put in a different example.)

I can't comment about rationalists and BDSM since I'm not a part of the latter community. What I do know is that subs tend to be just as happy with the arrangement as doms are and that a sub not being happy with the thing is seen as a bad thing.

Also, BDSM isn't just about inflicting (or receiving) pain for sexual pleasure. Aftercare is an important aspect of the relationships, from what I read.