Yeah, and before we continue I agree that guns and Mechs are arguably different enough that its not the best example either, but its almost the best case study we have to work with.
Well the problem here is not simply a matter of permits, Stone's ploughshares initiative was outright disarmament. Option 1 does not apply. Even the issue of registration and increased regulation - not even to the point of compensated disarmament - is sensitive enough that we're sitting here talking in circles. Now what would actual disarmament be like in the feudal 31st Century? The people who are giving up those weapons are landed gentry, pillars of the community, in fact with a strong use-case for those Mechs to put down bandits and for planetary defence - they probably helped Stone get rid of the Blakists and are still living in fear of reprisal. Remember this is a universe where more often than not a planet can be threatened by sudden Mech raids... and now Stone is saying "Give up the Mechs, trust in the State to protect you"! However rationally doomed to failure, its not unlikely that some people would have turned to their weapons when faced with such an ultimatum. We know this is a distinct possibility IRL, whether such actions make sense or not. In the BT world, perhaps these influential leaders hoped that the Republic could be compelled to come to a deal if they put up enough of a fight.
As for pirates - well, we know they exist, even those with Jumpships and Dropships. (They call em "pirate points" for a reason.) Don't think hillbilly survivalists or apocalypticists, think of hotter, wartorn areas of the world, where everybody contracts mercenaries private security contractors to move around town, and you try hard not to go outside of town without IFVs or MRAPs. That, I think, is the typical setting of a BT border world.