I think it depends on how you look at it. From my perspective:
pg added a useful feature, hidden comment scores -- then asks if you liked it better with or without them -- took that information into account along with data on comment voting patterns he has presumably collected since the change and made a decision.
What information could he possibly have taken into account that negates the fact that the poll option to bring comment scores back had more than twice the votes than the option to leave them.
What would pg's advice to a startup be in this case? Ignore your user's feedback and push the removal of feature (or push to leave the new feature, based on your stance), or listen to your users? I think he'd say to follow what your users want-- so why is he preaching one thing and practicing the other?
He could take into account the content of the comments on the poll, for one thing.
You're right that the results of the vote show a pretty clear 'winner'... I'm not sure that's the end of it, though.
If 1000 people wanted a specific feature in my app I would obviously take that seriously and consider it carefully. But it doesn't mean I have to do it, just that I should be paying attention.
I also think that the people who desperately want comment scores back are simply more vocal about it. I don't care all that much, and I don't remember if I voted in the poll or not (but I do remember seeing it on the frontpage). I think this should be taken into account, too. I'm sure 37signals gets thousands of emails asking them to add <pet feature>, and few asking them to leave that feature out. Just because your users want it doesn't mean you aren't still in charge.
Keep in mind that this is a man that tries to give you startup advice.