I actually agree with you inasmuch as I would say that Continental has no moral obligation to waive the change fee in the event of a wholly unilateral action by another carrier, for example if the Istanbul-Munich carrier had a mechanical problem which caused the cancellation (in such a case, I think it is clear that the purchaser assumed the risk by not purchasing a single interline ticket).

However, my take on the facts here was that the flight was cancelled for security concerns due to the bombings (I could be wrong, but this is how I read it).

Assuming this is true, I would think that Continental ought to have a slightly more emphathetic view toward waiving the change fee.