The damage was done... there's a ton of news stories about the outage, all covering the blackout protest.
There was some speculation in other communities that it was an intentional move on Reddit's part either to try to hide the protest (so they can say the drop in user activity was due to the outage instead), or that they were using the time to do something to counter the protest, but if that's the case, the news coverage is increasing the reach of the protest beyond what it might otherwise have had.
Honestly, trying to hide the protest by taking even more of the platform down is stupid. I really hope that this stuff leads to Reddit's user numbers dropping permanentally, but I doubt it as it seems like most subreddit only closed for 2 days.