TIME.com's technical team did detect and extinguish several attempts to hack the vote.
I don't think it's obvious that a hack went undetected by Time and gave the vote to Moot. What seems more likely to me is that more people voted for him.
Clearly Moot isn't actually as influential as an individual as, say, Barack Obama. But he represents the power of the internet masses, whose influence is proven by his victory.
But they gamed the whole vote not just his position.
The first letters of the first 21 names still spells:
"Marblecake also the game"
All of the top 21 are in those positions because of the engineering of Anon. - so, basically the vote is worthless.
Not so much the masses behind him but a devoted few :)
By doing so, Time has probably averted negative hacking, social engineering campaigns against their many web properties (e.g. How can 4chan's followers argue with the results?) It is a bit, tongue-in-cheek, though - they obviously did not drum it up (in the announcement) - as if someone like Obama had one.
That argument doesn't account for the rest of the hack. We have already had detailed explanations of what they did to 'extinguish' the hack from the hackers, and also how they got around the trivial upgrades to security. That acknowledgement from Time is denial, plain and simple.