I'm sure the doctor wouldn't prescribe anything that is going to be bad for the baby. If the drugs were worse then the illness, you would have to believe he wouldn't have recommended them.

If he is only worried about your core body temperature, try asking him if taking panadol will be sufficent to bring it down and leave the antibiotics till last. I had a flu shot in my first five weeks at my doctors request, as much as I didn't really want to, I felt it was best for baby and me.

Good luck and hope you feel beter soon.