It would not bother me so much, in principle, if the actual winner didn't follow the votes. Because it was going to go into the 'canon' and CBS would ultimately have to approve it, and CBS may not have cared. And I wouldn't blame Cryptic (much less denounce the game forever*) over what CBS decided, because it's not like they can control that.
That said unless CBS also had a hand in the second, third, fourth and runner up winners (and I don't see why they would, though maybe they did I don't know) I can't see why they wouldn't take the votes and ratings into account. Because otherwise, as said above, what was even the point of having them?
Incidently, the STO forums are pretty pissed at the winner, too. So it's not just this band of nerds.

*For the record, I do enjoy the game, and don't think it's 'crap' or 'rubbish' as others do (and please let's not derail this into a G&C level thread). Still, there are plenty of legitimate gripes about the game that could turn people away which have nothing to do with this contest. Like how they can release new Federation ships and costumes every couple of weeks, yet the Klingon side gets jack and shit despite many promises to give the KDF some love. Naturally, KDF players and even just those who like to dabble on the KDF side are pretty pissed over that.
Who knows, maybe the upcoming Season 4 update will finally give the Klingons some much needed loving, from ships, costumes, to actual content that isn't just straight PVP. But I don't think a lot of people are holding their breaths for that one.
"How can I wait unknowing?
This is the price of war,
We rise with noble intentions,
And we risk all that is pure..." - Angela & Jeff van Dyck, Forever (Rome: Total War)
"On and on, through the years,
The war continues on..." - Angela & Jeff van Dyck, We Are All One (Medieval 2: Total War)
"Courage is not the absence of fear, but rather the judgment that something else is more important than fear." - Ambrose Redmoon
"You either die a hero, or you live long enough to see yourself become the villain." - Harvey Dent, The Dark Knight