Murmurs are very common. I had one when I was a kid.
They can indicate more serious conditions like hypertrophic cardiomyopathy, but from the sounds of it you're well on top of your condition and if you had that I'm sure your GP would have told you about it by now.
These are the Class 1 requirements:
http://www.caa.co.uk/docs/49/SRG_Med...%5B2188%5D.pdf
If it's not listed, it can't be used to disqualify you. That's the theory anyway.