I never got injured, and I'm sorry to hear about your injury, but this is my 3rd attempt at completing the C25K program. I quit the first time because I went on vacation and life got into the way when I got back and started a new semester at college. That first time I got to W5D1 but never ran it. I'll admit that the 25 minute run also intiminated me so I kept putting off week 5. The second attempt was outside just as the real winter weather started hitting the East Coast. I started over and finished week 2 and then couldn't stand the cold anymore (that was in December). Finally, 3 weeks ago I weighed myself and although I'm not overweight I was suprised by the numbers, I was almost at my heaviest weight ever so I randomly decided to do W5D1 out of the blue. I suprised myself by completing it without having any breathing problems and decided that I'd continue. Today I'm doing W8D1 and have no plans on quiting this time!
I would say to go ahead and take the rest that you need. You dont want to make the injury worse. Visit the doctor and dont worry about the program until you feel better. Then jusmp into whatever week you feel comfortable at.