I'd get the opinion of another doctor. If her nasal drainage is discolored (vs. clear), that's usually sign of an infection. Unless you're giving her Zyrtec-D (D for decongestant), I'm guessing it's not having much of an effect.
As for swollen tonsils - they are part of the lymphatic system and enlarge when they're fighting off an infection generally.
I'd really encourage you to see another pediatrician and get a different opinion. Not to say yours is wrong, but it can't hurt.
Or, if you can see a specialist without a referral, I'd make an appointment with an ENT (otolaryngologist, Ear Nose Throat specialist) ASAP