I doubt that having coeliacs would be a bar for a career in flying but the military can be a fickle lot and especially for the more desireable functions where they have more candidates than places they could use it as part of their selection criteria.
An awful lot of good things can happen before your daughter is old enough to have to make any career moves and something better than a career in the military may well be on the cards.
More information on this website:
http://www.coeliac.co.uk/