It's call office politics and pecking order. And omega dog will be treated like an omega dog unless that omega starts acting like an alpha or beta. I find that working in large IT departments is very cliquey. You're both part of the clique and prosperous or you're not. And just like any group environment you have your three basic personality types. You have the Alpha or Leader, the Betas or followers, and you have the omega or the token beating post. Don't let yourself become the omega, take control and let them know that they're going to get their virtual faces beat in if they don't stop. I'm not advocating violence, especially in the work place, but you also need a working environment where people aren't going to pick on you all the time. But if you whine and cry or go above peoples heads all the time it will just get worse.
Personally here's how I would have handled the conversation.
Other guy: what, you're gonna be a MS dog?
Me: You know what? If you want to get your rocks off toying with Linux then you go right ahead, but as far as the industry goes, both operating systems are of equal importance. And on another note, what do my career goals have to do with you?
Then I would have left the office. My guess is that he'd be in my office in at some point to apologize and make friends. Remember, people want confident friends not wishy washy friends. They want people they can count on in a tight situation. My comments above would have told the other guy that I am the kind of guy who will stand behind my friends if they're in a pickle.
The point being that I set my rank, I let him know that I wasn't about to take any of his crap. In any situation where a person is placed into a group every person in that group is going to throw out their own test to set their social rank with that person, it's human nature. You just have to know how to respond to those tests to set your own place in that social ranking system. Basically, don't show weakness. And lastly, NEVER try to take the alpha spot unless you KNOW you can hold the alpha spot, because if you get hostily dethroned you are done. You might as well find another job, because working experience there will be no fun at all.
-Al