T.A.
I did the same thing with both my children. I did stop breast feeding at five months with my little boy and three months with my little girl. And believe it or not my oldest child stays sick more than my younger one. But if she doesn't have a problem with stopping the feedings, then I would stop. If only to make things better for you. You need to be healthy for her.
I have always taken my kids temp under their arm. Seems to work better for them. My pediatrician does say to add a degree if taken under the arm, but has never said anything about taking one away if temp is taken rectally.
Hope this helps.