If this was actually a case where a pilot was taken ill, the I can sort of understand EKs position. Are they supposed to have backup pilots at every outstation?
That is the risk of running a transportation company. EK may make a business decision how to deal with sick calls at the outstation. But that is not of any concern to the passenger. He paid the ticket and expects a transportation from point A to point B within the scheduled time.
If the EK business decision turns out to cause a delay of more than 3 hours -> then EK has to pay the price.