That's because they are both sharing the same port.
Many USB swipe card readers also share the same port, however, you can disable the keyboard in Windows rather than the BIOS which should allow the card reader to continue functioning.
As a final resort a serial device like this one would surely not be affected by disabling the keyboard communication port:
http://www.e-scan.com/profiles/msr100.htm
regards,
Philip T
*****
Added:
Use DevCon (from Microsoft) to override Device Manager, & enable/disable any device you like.
http://support.microsoft.com/kb/311272
Devices will probaly not be re-enabled by default on bootup, so it may be wise to create two simple batch files (one for enable & one for disable) & place them on your desktop for easy mouse access.
Also ... you may want to create an auto logon script should the keyboard be unaccessable for Windows user password entry.