I personally did not need the extension. Found a MIT link that showed how to remove, but for some reason I cannot post the link here, so the steps are below. I only did the uninstall and the prompt was removed. I'd assume you'd be able to re-download the application if you needed.
Note:
There is a downloader script in inside /opt/cisco/vpn/bin , so you may be able to re-download it using that.
To remove manually:
$ sudo /opt/cisco/vpn/bin/vpn_uninstall.sh
If you still having trouble and/or the new Cisco Anyconnect installation complains that you have a version installed, follow these steps:
Enter these commands to clean out the old Cisco VPN kernel extension and reboot the system.
		sudo -s
		rm -rf /System/Library/StartupItems/CiscoVPN
		rm -rf /Library/StartupItems/CiscoVPN
		rm -rf /System/Library/Extensions/CiscoVPN.kext
		rm -rf /Library/Extensions/CiscoVPN.kext
		rm -rf /Library/Receipts/vpnclient-kext.pkg
		rm -rf /Library/Receipts/vpnclient-startup.pkg
		reboot
If you installed the Cisco VPN for Mac version 4.1.08005 package, enter these commands to delete the misplaced files. The deletion of these files will not affect your system, since applications do not use these misplaced files in their current location.
		sudo -s
		rm -rf /Cisco\ VPN\ Client.mpkg
		rm -rf /com.nexUmoja.Shimo.plist
		rm -rf /Profiles
		rm -rf /Shimo.app
		exit
Enter these commands if you no longer need the old Cisco VPN Client or Shimo.
		sudo -s
		rm -rf /Library/Application\ Support/Shimo
		rm -rf /Library/Frameworks/cisco-vpnclient.framework
		rm -rf /Library/Extensions/tun.kext
		rm -rf /Library/Extensions/tap.kext
		rm -rf /private/opt/cisco-vpnclient
		rm -rf /Applications/VPNClient.app
		rm -rf /Applications/Shimo.app
		rm -rf /private/etc/opt/cisco-vpnclient
		rm -rf /Library/Receipts/vpnclient-api.pkg
		rm -rf /Library/Receipts/vpnclient-bin.pkg
		rm -rf /Library/Receipts/vpnclient-gui.pkg
		rm -rf /Library/Receipts/vpnclient-profiles.pkg
		rm -rf ~/Library/Preferences/com.nexUmoja.Shimo.plist
		rm -rf ~/Library/Application\ Support/Shimo
		rm -rf ~/Library/Preferences/com.cisco.VPNClient.plist
		rm -rf ~/Library/Application\ Support/SyncServices/Local/TFSM/com.
			 nexumoja.Shimo.Profiles
		rm -rf ~/Library/Logs/Shimo*
		rm -rf ~/Library/Application\ Support/Shimo
		rm -rf ~/Library/Application\ Support/Growl/Tickets/Shimo.growlTicket
		exit
Finally this.
sudo pkgutil --forget com.cisco.pkg.anyconnect.vpn