Without knowing the shape of her body I vote that she is not fat. 5'5" and 125 lbs is not fat. Keep in mind also that muscle weighs more than fat. She migth be ripped if she works out as much as she says she does. Also a 26" waste is not very big at all. 32C is also very nice. She seems to have a very compatible personality to you which is important as well. It all depends on what you are looking for in a girl for looks. If you are looking for perfection, Playboy type, she may not be it. But a size 6 is below average as far as women go.
My wife was 5'3" and 97 lbs, 34C since I met her 9 years ago. She is not sick looking but she is tiny! Her wedding dress was a size 0 and still had to be taken in. If you add 2" to her and 28 lbs she would still look good and not fat at all. She is now almost 4 months pregnant and is now up to 106 lbs.
If you can find a girl with her measurements that you click with, she supports you and your hobby and tries to make you happy (by cooking you pasta on Thanksgiving cuz you don't like Turkey) and she needs to lose 3 lbs, count yourself lucky.