Sridhar,
If there are just two devices on the subnet - the 3845 and the 6509, then having an access port as compared to a routed port is almost the same. In fact, creating a routed port internally allocates a separate hidden VLAN on the 6509. Still, I would personally choose the routed port. If nothing else, it is not being controlled by STP anymore, and it does not send Layer2 management protocol messages to the router that is incapable of processing them.
Best regards,
Peter