Doing too much too soon, before your body has had the chance to adapt to the rigors of running is one of the biggest causes of running injuries. Running is evolutionary and you cannot rush the process to adapt. That being said, with any injury it is best to avoid running until your symptoms have completely resolved for a solid week. My running coach told me that injuries start out like a chip in your windshield, if you take the time to get it fixed now you may be able to avoid the windshield developing huge cracks which in turn means you will need a new windshield.
While runner's knee is very common, also know that the knee is the convergence of major muscles and connective tissues in the leg and this could be something you have not considered.
I wish you a SPEEDY recovery!