The group as a whole has to be aware of it to tolerate it as a whole. This is not the case with a lot of Reddit users. Personally, I didn't even know this happened until these articles started popping up.

If one aggressive subreddit takes irresponsible action, is that fair to say "Reddit did 'X'".

Or is it more accurate to say "the subreddit /r/findthebostonbombers of the Reddit web site did 'X'"?

I would argue for the latter. Granted, the mainstream media is unlikely to make the distinction or care, but it's an important difference.