Couple of things. Loganair under the auspices of BA livery operate the LDY-DUB route...quite successfully too. Also, Derry isn't the only part of Norn Iron where rocks are thrown. If that was a deterrent to airlines operating here, there wouldn't be the need for one tiny airfield never mind the three that there are now.
I was in Derry last week, and it would seem from both local media and comments made by councillors on the airport committee that the runway extension will go ahead, though terminal development will be delayed for a while. I think in the not too distant future the council/airport will be able to call RYR bluff. Furthermore a new aviation company (Foyle Aviation) doing paintsprays and the usual maintenance will be up and running by Spring of next year.