Well I think this is a lot like when I was in High School. The term Freshman isn't in an of itself a derogatory term, and was never thought up to put anyone down. It's just the jerks who decided to turn the word into something mean, and use it hurtfully. I feel like "noob" or "newbie" if you will, is a very similar word, both in necessity of invention and derogatory usage.
So....basically, don't be a jerk, and it's not an offensive word. "Noob" just means new at something. That's not offensive, that's a fact. Any word can be offensive and derogatory if that's your intent speaking it. I can call someone a really nice person, but if I say it sarcastically I'm being mean. I can tell a girl she looks like a model, but if I'm saying it to infer that she's less because she doesn't look more like "normal" girls, I'm being mean. You feel me?