I am in the same position with a knee problem which reared its head after the last long run. I know I should defer but as I deferred last year well in advance because I wanted to run this year. I had not factored in injury. So I am giving up my chance to run it at all. Will have to re-enter the ballot again (and again).
Marie - please read the thread on the injury section on the forum here which talks about hip impingement and all the necessary surgery that is involved. Mind your hips and don't get to the stage where that is necessary. Some of those poor guys have been told they can't run again.
I am with the don't run camp I'm afraid. But it's so hard for you that your decision has to be so public!. I agree with whoever said to be honest with the doctor, then at least he will make the right decision for you. And will remove a lot of the emotion (or guilt!).
The fact that it is sore every day and flares up during exercise or just after, makes me nervous. If you get to the start line, I doubt whether you will drop out, you will grit it through in pain or hobbling to the bitter end. And thats a long way for your poor knee.
You have improved so much under the Sam's training it would seems a shame to jeopardise all that potential. Get the knee sorted and find another marathon. On one condition, you start a new thread for that one so we can all keep track of your amazing improvements!