Freight has been doing that when it works best for donkeys years.Anyway freight services do have to cross below York anyway and now it looks like they might be re-routed through the main train shed!
The flyover will be an order of magnitude cheaper than changing the line to pair by use rather than direction.It's merely just a thought about which would be better considering the x amount of millions it will be for this proposed 2/2.5 mile flyover at Northallerton.
The flyover solution is probably several hundred million. What you've suggested is easily going to break a billion once you factor in all the changes to Thirsk, the OHLE, switches and crossing, signalling etc.