If you get the interview then this issue will of course come up, BUT the fact that you got an interview should show its not such a big issue with the airline concerned.
Some airline management won't even give your cv a looking for an ops job being a pilot, others will.
Before the question is even raised, make a case for yourself that you want to do more in the industry and company in question than just eventually fly planes. Give yourself something to fall back on when it does come up.
Viking9: I think you have a very valid point but maybe being a bit harsh. From my experience gonnabe pilots are more motivated, accurate, knowledgeable and interested in the job than your average ops guy/gal. And, once they do get onto the flt deck (perhaps with the same company), will have a better understanding and appreciation for your job.