I think the reason that the lore is so different is because Riot actually didn't write Varus' old lore, but rather it was written by Gabe and Tycho from Penny Arcade [(http://forums.na.leagueoflegends.com/board/showthread.php?t=1984973)]
After all of this I can't help but feel that they wanted to distance themselves as much as possible from the PA version. It is the only reason I can think for such a radical and unneeded change to his lore.
Or...
They just had a new narrative direction for Varus in mind that they themselves felt passionate about and figured they're go with it. Not everything has some convoluted reason behind it, sometimes it's literally a case of "Hey I've got an idea" and the process of then having that idea be realised.
You can only believe this if you think the old Varus lore was good. And I went to the mat with people who (i think) had some veiled homophobia about his new lore. But the Lore was boiler plate. It was the sketch you have for a character you haven't yet developed.
The new lore ties in with the other characters that have Darkin storylines. They've essentially created a new race. I expect the new Varus lore will tie in with a larger event soon, but in no way do I see his rewrite as anything but bringing Varus into something larger than himself. It's Taric pt. 2.
They say in that post that they teamed up with them to create the teaser and judgement,that means the regular lore was still written by riot and they still had a hand in doing the other stuff.
