Jeez guys... Leave the Wiz*gizmos for arduino kiddies. If you that much need the ETH and want to spend the extra time and effort, do it properly using a MCU with integrated ETH/MAC. It is not magic to make a custom ETH application, just add the ETH/PHY chip and connect it up. It's not even complicated. There's enough code to get it up and going already written, no need to reinvent a TCP stack.
Leaves you debugging just one faulty firmware: Your's on the MCU, not two (MCU and the wizmo module).
In that case, I'd redesign the front panel PCB to accomodate for all the HW updates of the FP.
STLink is of course the recommended way, using the bootloader is just for the situations where you want to get mad quickly.
You could also use any of the free toolchains for STM32, no need for linux either. AC6 Workbench, Atollic,... Will get you allso full debug support on the MCU - which I find mandatory when developing such complex applications.
Good night!
PS: Yes, I hate those half arsed solutions.