Being as you bought him from there it is worth mentioning the problem. Pets at Home, despite of all their faults, they do (and so they should) tend to offer free vet care if you bought your pet recently. I hope eight weeks is considered recent enough.
Good luck. Please don't be afraid to mention the meds advised, or to mention that an awful lot of pigs have been having respiratory issues from Pets at Home. I am the sort of person who rarely makes a complaint, but if you are firm with them that you feel the issue is down to where they source their guineas, they may go the extra mile for you, and I would certainly be complaining if I were in your shoes.
Hugs and good luck xx