Well, your body is naturally immuno-suppressed during pregnancy since your baby is basically a great big ALIEN to the rest of your body.
Your body is struggling between trying to feed and sustain it and trying to kill it. Kinda freaky, huh?
So, it's not surprising that you're coming up with an increase of infections during pregnancy. Trust your doctor... double check the FDA pregnancy category of all drugs you take... eat healthy... take your vitamins...
In general, your ob is worried about your health, as well as the baby's. But your's has to come first, because without you there is no place for the baby. Sometimes that means docs have to make decisions that might seem contrary to common sense... but you can't let an infection fester since it might spread and become systemic and could cause severe illness.
I hope you're feeling better soon.