Thank you in advance.
Any potential security etc. risks arising from the conflict you refer to are confined to the close proximity (max. 20 miles) of Turkey's borders with Syria and Iraq (on the Turkish side of the border, that is). Istanbul is literally a thousand miles from there!
There should be no problem to transit through an airport which is located in the European part of Turkey..
Unless you're flying Malaysian Air, which seems to be dumb enough to fly over a war zone, you'll be fine. The risk would be if you were flying over Syria and some bozo mistook you for a military cargo/transport plane.
Turkey is generally safe.
