It depends on the people.
As someone previously pointed out, if the pub in FA was firing at a shielded ship you could as pilot launch a tyco and destroy the shields so that the FA shots arn't wasted.
Additionally, boost drifting cancels/resets FA, so pilot CAN in fact lock out the gunner.
There is always the option to type out "please stop firing forward artillery"
Someone said "but can't type because too busy being shot by enemy ships". To this point I have to wonder. Even veil enemy ships can swarm by the 20's around and barely put a dent in my ship. And when they do, in a properly loaded out RJ you can destroy them all instantly at any point in time.
While I may not do it that often I join public matches/open my RJ publicly sometimes. Most of my experience has been i'll find a ship doing missions that is using void hole, seekers or munitions vortex if i'm semi lucky and they either say nothing or are happy when I enter FA and destroy some things. If i'm really lucky i'll find someone using tether properly. Recently I was doing some runs set on public. The first run one person joined and jumped in FA, we killed everything quickly and I asked if they could forge between missions (artillery cheap shot, so during a mission it never ran out). They said "sure". The next mission another person joined and after a minute asked if we were friends. When I said no, this new pub said "oh, but you guys are so well coordinated".
Moral of the story: RJ is simple and it really only takes a few words to do thing right.
I'm not totally against setting permissions, but I think it fly's in the face of DE's stance on voting in missions. Too many opportunities to troll from host/players to justify a small potential gain if at all. Most missions I encounter have no problems so implementing a system that might solve those few problems could mean it introduces more than it would solve.