I doubt anyone would make a (non-spam) system that rewards people just for signing up. The site creator would be careful to reward only meaningful actions. So this isn't realistic.
>> It further encourages behavior designed to obtain badges.
That's the whole point of the badge itself though - encourage a particular type of behavior. I don't see this as a problem either.
>> bill it as a more generic hub for sharing information about what users get done in a given application
Very interesting take on the idea.
For example, HN could have a "1000 Karma" badge, which would be meant to encourage thoughtful, intelligent submissions and posts. People could instead say majority-pleasing things. Even worse, people could collaborate to vote each other's posts up. Get 32 such people together, have each make 32 posts in a topic that left the "New" page without getting any votes, and presto! 1024 Karma for All!
There are many variations on these themes. Badges (in social/multi-user settings) largely fail at getting people to do what you want, unless what you want is for people to waste time getting badges.
Now, in a closed system, this can be minimized: people who would normally read and post on HN are less likely to resort to these shenanagins, and others just wouldn't care. The aggregator gives them a reason to care.