I do not see any problem. I support many customers, and a few of them give me their RSA token to connect to them using VPN.
I create multiple profiles in Cisco VPN client, different profile for each customer. These profiles are in pcf files.
Edit the pcf file that correspond to those using hardware token using notepad, make sure you have
SDIUseHardwareToken=1
Details:
http://www.cisco.com/en/US/docs/security/vpn_client/cisco_vpn_client/vpn_client500_501/administration/5vcAch5.html