First, I have to say that the real history of the NEOC logo predates me; I haven't been around this game much longer than you have. As you say, I guess people just saw the logo and it looked like a troll, and so it became. But trolls have not always been viewed in a negative light. There's a city in Sweden called
Trollhättan, and I remember seeing the window sticker shown on that page on SAABs back in the day. Also popular when I was a kid were
these dolls, which were known in my neighborhood as "wish-niks", but other people called them trolls. It's true that the trolls in Tolkein's work are best avoided, and the troll in The Three Billy Goats Gruff is a baddie, but even ogres can be viewed as lovable, as we see in Shrek.
In fact, based on the etymological info provided on wikipedia, the notion of an internet troll may not be earlier than 1992, and the origin is likely not the creature of folklore, but rather the verb as used in fishing, to drag a baited line behind a boat. This makes sense, as an internet troll isn't doing something like demanding payment to cross a bridge, but rather tossing something out there to see what he might catch.
That said, the origin has been made blurry, and thus people tend to associate someone disingenuously looking for an argument with flat-footed cave denizens. As a result, it's quite unfortunate that the string-O division of our national association is known as the Little Troll Program. Srsly?