I know when running freepbx fop2 will auto-generate extensions each time it is started.

the problem here becomes that freepbx has no way of re-starting fop2 when changes are applied ie when new extensions are added.

It would be nice to have better freepbx integration.

and finally maybe a freepbx module that adds a Fop permission drop-down to the extensions page in freepbx.

I think it would need to be the freepbx guys that done this request or you would have to change the engine file every time you update freepbx, looking at the file it shouldn't be to hard for them to do

[added]
here is something to get you started

reload_fop2() {
	ps -C "fop2_server" >& /dev/null
	if [[ $? -eq 0 ]]; then
    		/etc/rc.d/init.d/fop2 restart
		echo "FOP2 was restarted"
	else 
		/etc/rc.d/init.d/fop2 start
		echo "FOP2 was started"
	fi
}

you could call this via reload_fop2 in the engine reload script