There have been enough of these incidents to start thinking about it from a serious engineering standpoint. The plane is going down if the pilots can't see, so the number 1 problem is to create visibility in the cockpit - you can't rely on open windows or port for that - the best way is to create a pressure differential between cockpit and cabin, meaning somehow in freighters the cockpit itself has to be inside its own pressure vessel - that would not be too hard to implement with the proper bulkheads and vents. In a dire emergency one should be able to isolate the cockpit and generate enough pressure in it to force the smoke out into the lower pressure environment of the cargo cabin. A variation on the RAT could be used to generate pressure for the cockpit while the rest of the plane is at ambient atmospheric pressure. After some googling, it appears that even in submarines this is not exactly a solved problem. Time for the engineers to sharpen their pencils.
-drl