Do you "need" to run this year? One of the features of the London marathon is that you can defer your entry until next year.
I was in a similar situation last year as my running was hampered by a knee injury. I tried to get back into training etc as I really wanted to participate. However, I eventually realised in Feb that it wasn't improving and went to see my GP, and at the same time deferred my entry until this year. I can't adequately express the amazing sense of relief I felt when I completed the deferral - a huge burden was taken from my shoulders and all the stress just disapated away.
I've been back in training since the summer and I'm deep into my training schedule for this year's marathon with no issues and my focus on completing the marathon in a PB time, whilst remaining injury free. With hindsight, if I'd attempted to run it last year it would have been a miserable experience as I wouldn't have been able to train properly and would have probably ended up with other injuries as I tried to compensate for my weakened knee.