Fred and George didn't do it. They planted a story about Quirrel. Quirrel read the story and, seeking a way to get back at Skeeter, found out that Fred and George were trying to get back at Skeeter on Harry's behalf – but not that they had planted the story about Quirrel. So he offered to help them, and set everything up for Skeeter, then wiped their memory of everything they'd done to plant the story, which included the memory of planting the story about Quirrel.
I still can't see how publishing a stupid and incorrect story would have been reason enough to make people assume that Rita Skeeter had gone into hiding lest she faced Malfoy's punishments.
Canon!Skeeter would hardly flinch at publishing bullshit stories, and I don't recall hints in MoR that that trait was different - hell, she says her paper regularly throws around empty accusations of Death-eating, which sounds like a much more dangerous thing to do for a publication than fake marriage tales.
Update: Discussion has moved on to a new thread.
The hiatus is over with today's publication of chapter 73, and the previous thread is approaching the 500-comment threshold, so let's start a new Harry Potter and the Methods of Rationality discussion thread. This is the place to discuss Eliezer Yudkowsky's Harry Potter fanfic and anything related to it.
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven. The fanfiction.net author page is the central location for information about updates and links to HPMOR-related goodies, and AdeleneDawner has kept an archive of Author's Notes.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: