In El Capitan 10.11 it is no more possible to add files in /usr because of the new security protection.
I have seen the WWDC 2015 presentation « Security and Your Apps, Session 706 » that describes the new System Integrity Protection.
Files from /usr should be moved to /sur/local. OK.
Smart card reader drivers are located in /usr/libexec/SmartCardServices/drivers/. Apple only provides a CCID driver as ifd-ccid.bundle.
How can I install a new smart card reader driver in El Capitan?