Instead of bothering yourself with such a detail, why don't you at first apply to the airlines, and after being accepted just take this 1st medical Test. You ought to feel much better and you will not think so much about the running issue of yours, it's a small detail really.. But, if you shall still feel as not fitting in then just resign as I did for a while,but I'm a girl and at that time I thought I know no one out there and thought I really like to be with my mum around.
Certainly, you shall not be asked any questions regarding your running status unless you shall talk about it. Just apply and at latter take a test.