Not knowing the particulars about your card reader, I was wondering what drivers they use, here is someone chronicling their integration of "a" USB credit card reader
http://www.micahcarrick.com/credit-c...der-pyusb.html.
What I see there is it shows as a Human Interface Device (HID) but it got installed as a different resource than /dev/event.
So I believe this is your fundamental problem is how this device is getting mapped and recognized by your system. Was this the native way it got discovered? Was there any guidance provided by the manufacturer? Or did they not even say it was Linux tested?
I think the bottom line here is if you have something which is re-using /dev/event0, then that WILL cause keyboard events, because that's how all applications which expect the traditional keyboard are going to gain their input. The other problems here extend beyond an open command prompt, it could be so worse as sequences like CTRL-ALT-DEL or CTRL-ALT-F1 get misinterpreted.
So I'd diagnose if there were a more correct way to integrate that card reader into your system rather than try to stop or redirect keyboard I/O. Because the keyboard I/O should stay there and that card reader should not be interfering with it.