leave some freedom of choice please. - figuring out a suitable ship and weaponry that fits to a player is not a minor but a rather major part of the game.
imagine the game "mechwarrior" - which consists a LOT about anticipation and customizing your mech. - take away customizing the mech - and the game itself becomes boring. - take away the ability to customize your ship in freelancer and you ll loose a major aspect of the fun.
also - limiting everything to the faction is - frankly spoken..... a pvp server attitude; - in a negative way. allowing players to make up stories, backgrounds etc. for what they use is more RP.
to take your little example ( or one of them ):
the BHG capital ships do not have their own weaponry. - the NPCs use liberty capital ship turrets. the lore states that the BHG originates in liberty and that they employ very very tight bonds with liberty lawfuls. - all that points to the fact that they get their weapons from liberty - henceforth, they have ( or had ) no need to make their own ( if thats sufficient for an explanation about what weaponry they can use ).
this explanation is MUCH more logical than asking them to use zoner weapons by the way.
this example shows how much roleplay can clash with a pvp attitude. - and for many players, it is VERY little about stats on a weapon - but much much more about how they look ( its amazing how many players find looks at least as important as stats.... )
if you go the way about limiting stuff to the very end - you ll end up without even a choice in your own factions weaponry. - why say you can only use your faction guns - when the ID card clearly states that "level 8 weapons" are meant to be used on a particular ship? - even if i can mount lvl 10.
do you really want to fly around like NPCs? ( or in the case of the BHG warships - not like the NPCs )