Add option under subreddit setting that says something along the lines of, "don't allow content from this subreddit to be shown on the front page."

Edit: I meant "don't allow content of this subreddit to be shown on /r/all." It was a typo.

• An unexpected flood of users and content caused by a popular post can cripple a mod's ability to monitor a subreddit's content.

• Some reddits have shown concern about a sudden influx of frontpage r/all users reflecting badly upon their usual discussion. I've seen this problem combated by some mods giving popular posts a "Warning: All" tag.

• Some of reddit's communities would just prefer to stay out of the mainstream in general.

On the other hand, I could see some users feeling snubbed if they don't realize that the subreddit has enacted this option.