Sounds like a simple code change would have solved this: if a post has ever been stickied, it shouldn't be able to hit /r/all.
On the one hand, yes; I don't think the admins made that specific change, but they took away the ability to sticky normal posts, in response to T_D's shenanigans, ending the effectiveness of that tactic.
On the other hand, there aren't simple technological fixes to social problems. T_D's mods remained tricksy and continued to work their userbase to upvote and focus - in ways which didn't breach the sitewide rules on manipulation - and still kept hitting /r/all
Reddit could have simply banned T_D at any time. In the years since then they've definitely started banning subreddits for no good reason, but apparently based simply on how much upper management likes the subreddit. Presumably, T_D was not banned because upper management liked it.
You know, I had actually forgotten about the "sticky" thread issue. Goes to show you how bad our memories can be at times.
But yeah, using the sticky system to force posts to top of mind was super effective back then. It's all coming back.
https://old.reddit.com/r/TheoryOfReddit/comments/4fh8s9/this...
Normal humans tend to upvote things that are already upvoted. But normal humans don't tend to look at the incoming stream of posts.
Ordinary T_D users were refreshing the subreddit's front page. Mods stickied the posts they wanted to rocket to the top. This got them past the hurdle where very few people look at /new to give those all-important first few upvotes. Ordinary T_D users upvoted the stickied posts. The mods then unstickied them less than an hour later, because now they're "organically" at the top of T_D, and the upvotes continued to pile in, rocketing the post to /r/all
Meanwhile, all the other subreddits weren't playing this game, so their users votes were split across multiple posts on their subreddit's front page. And mods of other subs use sticked posts for administrative notices, which are worded as such and tend not to get upvoted much... but if you were to sticky a normal post, users would upvote it. But stickied posts aren't eligible for /r/all... unless you unsticky them. Oops! T_D successfully gamed that oversight.
EDIT1: Also... as the comments in the link above reminds me; it used to be that any post could be stickied, e.g. normal link posts. It wasn't necessarily clear that they were stickied posts. What changed after the T_D manipulation is that sticky posts were renamed "Administrative Notes" and had to be text posts and had to be coloured differently from normal posts. Before that change, they weren't distinguished that way. Now perhaps the subterfuge by mods makes more sense?
EDIT2: WIRED's postmortem on T_D - it was cunning mods, not bots.
https://www.wired.com/story/the-hate-fueled-rise-of-rthe-don...