Having a bias when doing a 'paper' is fine. It is, after all, her thesis, her opinion. If all 'papers' had to be 100% unequivocal fact, then only one paper could be written on any specific topic. It is the combination of experience, knowledge, opinion, and research into others work's that make up a well written paper, IMHO. The fact she has a bias is almost a prerequisite, not a hindrance.
And in so far as you attacking her, I would agree that if she were arguing her opinion on the war itself (antiwar), you could have at 'er. My problem is this: whether she took offence to it or not, I feel you went at her with an 'Anti-Academia' position, when she has expressed nothing but respect, tact, and professionalism to us. She could have come here and said, "The war is crap, make love not war, Bush is an arsehole, etc." but she didn't. You responded to her polite queries with an attack on Academia, and regardless of whether your postion on Academia is accurate or not, that attack was unwarranted and irrelevant.