Replace Windows USB Class Driver with a custom driver?

You're using libusb-win32 as a filter driver; that is, the HidUsb device driver is assigned and loaded for your device, but then the libusb-win32 driver is loaded on top and gives you unobstructed access to the hardware.

If you don't want a HidUsb (or any other class driver) to perform any communication "on your behalf", simply associate libusb-win32 as a device driver with your hardware. For this, you'd have to create an .INF file associating it with the VID/PID/Revision of each USB device. If I recall correctly, libusb-win32 even comes with a utility to generate such .INF files.

If you install this .INF file e.g. with PnpUtil.exe (available on Vista or higher), you might still run into issues where, although you're a better match than the generic HID driver, the HID driver is still selected.

The generic HID driver matches devices by their Compatible IDs (i.e. by a USB interface class) while you'd be matching by Hardware IDs (which have higher priority). However, Windows might give priority to other aspects, such as your driver being unsigned. Read: How Windows Selects Drivers

Luckily, even in that scenario, signing drivers with a self-generated certificate (use CertUtil.exe, MakeCat.exe and SignTool.exe) is not too difficult.