First is realizing that there are technical solutions. Some people say "you don't want technical solutions to social problems" but the fact that subreddits have no protection against brigading at all is a serious design flaw with reddit[1].
Second is some way to require subscription for some period of time for votes to appear or to count. The CSS-hack stuff was silly, and as someone who has been on reddit since its first year, I have never seen the CSS-side of reddit because I never turned it on.
One of the big complaints from the blackout was the complete lack of tool support and this is an example. Reddit tried to paper over the technical shortcoming with rules and social hacks but once different reddit communities who didn't like each other realized there was a way to attack each other they did so.
[1] to be fair I wouldn't have realized it either if I was in charge of the subreddit design
I think there's an interesting cultural weirdness about Reddit here. Part of the problem with brigading is that if you link to another post in another subreddit, you're already logged in and have exactly as much power to upvote and downvote and comment as you did on the subreddit where you came from. There's the entire "no participation" community-by-obscurity trick, where subreddit CSS hides voting links if the hostname is np.reddit.com (this is supposed to be used for translations into the hypothetical "NP" ISO-631 language), but the fact that it's a CSS trick points to underlying discontent.
On the other hand, Reddit is a great platform for small communities precisely because you're already logged in. I've never created a Lambda the Ultimate account and only think about it maybe once every six months, but I'm subbed to /r/types, so anything that flies by gets onto my Reddit home page.
I'm not sure how to reconcile these two problems. A client-side aggregator would solve the issue of visiting each independent site, but the shared login mechanism is also crucial, and is both a blessing and a curse.