On my blades, when use kickstart, I use the install --firstdisk option to force th einstaller to use the local disk by specifying the driver of the internal disk controller. Obviously this does not work when you use boot from SAN, but if you are installing to local disk, this should work.
Example:
install --firstdisk mptsas
You can also add the --preservevmfs switch if you are super paranoid, but if the local disk has a VMFS, your scripted install will probably error out.
Another thing that I do is use the Image Builder CLI to create a custom image that has the FC HBA drivers removed, so the installer can't possibly access the FC LUNs. After ESXi is installed, during the firstboot section of the kickstart script, I install the HBA driver. Again, if you are booting to SAN, this won't help.
Example:
# FirstBoot Script
%firstboot --interpreter=busybox
# Enter Maintenance Mode
vim-cmd hostsvc/maintenance_mode_enter
############################################
####### Install/Configure Drivers ##########
## Install QLogic HBA driver for FC-FCoE Adapter
esxcli software vib install -d http://x.x.x.x:8181/Drivers/vib/qla2xxx-934.5.6.0-offline_bundle-887798