In general, good PTs tend to distinguish between two kinds of people. Some clients will be extremely sensitive to pain. These folks will, in general, benefit from being told to exercise even when it hurts a bit, as it will prevent muscle loss &c. Other clients will be significantly less sensitive to pain (case in point, I once finished a 10mi cross-country with a piece of barbed wire lodged in my calf - not because I'm so darn awesome and tough but because I simply have a reasonably low pain threshold). In my experience, having worked with some really good ones, they try to calibrate their advice.
Now, chondromalacia patellae is one of those things where there is no clear 'best treatment'. In general, there are two main schools. One teaches RICE and slow resumption of activities ('build-up'), another teaches to keep as close to your normal activity level as you can ('scale-down'). Generally, the best approach for you will depend on two things. One, can you, in terms of fitness, afford some downtime? Some people can easily sit out a few weeks and get back to where they were in weeks. Others can't get back so easily, and you know yourself better than we do, I'd wager. The other is what you have available. If you are near a good gym, this would be a great way to do some of the cross-training most athletes skip! Alternatively, a good personal trainer can create an exercise plan for you that involves all the elements of running but those that would irritate your patella. Ultimately, neither of these is curative and the question is what to do while your condition resolves itself peacefully. Diclofenac potassium and naproxen are two wonderful NSAIDs (you're going to get a lot less effect from ibuprofen and virtually none from paracetamol and aspirin) for this sort of pain that can make moderate exercise bearable. Of course, this is also a time when you ought to consider whether you're training too hard/the wrong way, since CMP is most often an overuse injury.