I am not sure if this is already implemented, but...

I believe that while your loading a new sector, the "clock" for getting a fast delivery bonus on a trade mission, should be stopped. I am not sure if this is already implemented, but if it doesn't take too much resources to do so, it just makes it more fair for people without "supercomputers".

SuperFreeza

At the loading screen, it's not just loading the geometry of the sector. It also has to get the position and direction and other info for every moving object in the sector, and who knows what other synchronization is being done to enter the sector...

But you're right - if you are the victim of long-loading-screen, for whatever reason, some consideration should be taken in the mission computer. I think once they smooth out the lag issues, this problem will be less noticable of an issue.