Go for option which is cheaper. I just purchased emirates ticket from travel agent which was 2,000/- expensive than emirates online ticket price. I prefered to spend 2,000/- extra because that is non refundable ticket and I have to visit Singapore in March and I applied for visa through same travel agent.
In September I bought Airasia ticket online, not face any issue with it either.
Emirates has advantage to book online and pay either in Allied bank or in their office without extra charges.