Please always follow your vet's prescriptions and DO NOT skimp on antibiotic courses. If the antibiotic doesn't have any impact at all after one week or it comes back again as soon as you stop (or shortly after), please see your vet again and discuss alternative avenues to investigate. This may be a different antibiotic or investigating other potential causes.
My own guinea pigs often needed 2-3 weeks of an antibiotic to get on top of a respiratory infection; the symptoms would go away only in the second week and then they needed some more days to make sure that the infection would be cleared fully.
I have got guinea pigs of mine on several months of a much stronger antibiotic. It has made the difference between putting to sleep and living 5 1/2 years longer to nearly 7 years of age. Soft poos and support syringe feed during part of it where something I didn't mind at all. It didn't do any permanent damage considering that the piggy in question lived the equivalent of over 50 healthy human years longer.
A one week course can often be too short to clear an URI. As URI can kill or permanently damage the airways if it is un- or undertreated, coping with a temporary tummy upset is sufficient reason to abort the antibiotic. I have adopted a guinea pig that was finally after two years of respiratory issues diagnosed with both upper and lower lung disease due to a not properly cured URI earlier in life.
In order to bolster the guts, you can give a pinch of probiotics either 1 hour before (US recommendation) or 1-2 hours after you give the antibiotic. You can get probiotics from a pet shop or order a god brand online.
Probiotics, Recovery Foods And Vitamin C: Overview With Product Links
Please have her vet checked to see whether she has still got a residual bacterial infection or whether you need to research for sensitivites to hay dust, pollen or perfumed products with your vet.