One of my dissertation reviewers wanted me to remove a humorous aside from my dissertation because he didn't think academic writing ought to be enjoyable to read. Or so I said to my advisor when I told him about it. I said that I would to refuse to remove the paragraphs just because some humorless ogre didn't like to laugh; I had my principles, after all.
My advisor never did tell me whether he thought the paragraphs should be removed or not, all he said to me was that I was losing sight of the goal, which was to graduate --not to publish a dissertation that I personally liked. He was right. I wasn't standing on principle, I was just being stubborn.
It is human nature to confuse stubbornness with principles when we want to be obstinate, and to confuse principle with stubbornness when we don't. There are various things we can do to help avoid this mistake. Ask yourself, "Who am I doing this for and what does it accomplish?" Or maybe ask yourself, "What principle, exactly, am I standing up for here, and is it really a noble one?"
But there is a simpler test that is extremely effective. If you have chosen to take a stand on something, examine your feelings. Do you feel righteously defiant? If so, you are probably just being stubborn. After all, righteous defiance feels good and we do wrong because it feels good, we don't to right because it feels good --Hollywood ethics to the contrary. We aren't stubborn for no reason; we are stubborn because it gives us a feeling of smug satisfaction. If you have that feeling, maybe you should reconsider.
The opposite is also true. When you have taken a stand and you are wondering if you were too inflexible, too stubborn, then ask yourself, did the stand cost you more than you wanted to pay? Do you wish that you could just get along rather than being defiant? Then there is a good chance that you are standing on principle. Don't give up now.