What firmware are you using. If the firmware has its own bootloader, then most likely it has its own method to trigger it. So maybe some are simply using the HWB pin to always trigger the bootloader, where the bootloader will determine whether it should jump to the app or run the bootloader app (depending on keys pressed, etc). Although I'm not sure why the boot reset vector fuse would not be used instead, if that was the case.
The fuses cannot be changed via the factory usb bootloader, so out of the box the 32u4 is set to use the HWB pin and the reset vector is 0. In order to run the factory bootloader, the HWB pin needs to be low when the reset pin goes from low to high which basically changes the reset vector to the bootloader and the factory bootloader runs (and remains running).
If you do not have other means to program, then the factory usb bootloader will have to be used and a means to trigger it- the HWB pin. A weak pullup would just keep the HWB pin high- I don't know what value, but would not take much- 10K, 47K, 100K, whatever. When you want to run the bootloader, pull the pin low before the reset. I don't know what your row/col scheme is, but I would guess the additional weak pullup should be harmless in most cases.
If you have a programmer for the mega32u4, then you can do whatever you want- use firmware that includes a bootloader, change the boot vector as wanted, eliminate the HWB usage, etc.
Your schematic - the HWB should have a resistor from it to Vcc, which means its pulled high. The switch is also connected to HWB, and the other side of the switch is connected to ground. In other words that 10k resistor needs to move.