First of all, as you probably noticed Flow Control on ESXi operates in autonegotiation mode by default, so it will only be active if the physical switch supports and enables it too. Some good information on the topic in general: http://rickardnobel.se/esxi-and-flow-control/
As to why you can't change the parameters, check if there is an updated driver for your NIC. Use ethtool -i vmnicX to see which driver version is currently running.
The ESXi HCL lists a few updated qlcnic async drivers:
The latest one being this qlnic 5.1.157:
https://my.vmware.com/web/vmware/details?downloadGroup=DT-ESXI5X-QLOGIC-QLCNIC-51157&productId=285
qlcnic-esx50-5.1.157-1089431.zip
Release Date: 2013-04-12
Build Number: 1089431
Update the driver and see if you can configure the pause feature then.