No, you're right. Wages are paid for all employees at the end of your business week, regardless when they were hired within the week. I guess it's a programming thing.
If you really count on every penny, disable to automatic hire function and only hire those people after your business week has ended. You can even activate flightplans (with a 3 days delay) and then assign the pilots later (e.g. after the end of your business week).
But that won't kill your business. If it does, the reason might be found somewhere else