The straightforward way would be to modify the bootloader code respectively. You didn't tell why this isn't an option.
If it's possible to fake a GPIO input to the bootloader depends on it's implementation details. It might work if it relies on POR default GPIO register settings and doesn't reprogram the pin to input. In this case an output state set in the application would be preserved.
The backside when jumping into the bootloader is, you possibly need to restore various registers to expected POR conditions. Jump anywhere in code space is however possible, at least using inline assembly code.