Personally, my own views on factions policing independents is that factions shouldn't really have the right. In the instance of Junker powergaming disturbing Kusari (just FYI, the bounty issued by the AFA on the Congress has nothing to do with my opinions of Junkers in Kusari. My talks with Zelot, Baconsoda and Griz have.) it's compounded by that there are relatively few Farmers Alliance, Hogosha and KNF types to deal with what is actually a huge amount of Junkers.
As faction leader, while I neither want nor believe I have the right to bark orders at people, I do want to help those who I RP with/against. A happy enemy is an enemy I can have fun planning events with.
And Tink, while there's merit in that "It's not their Kusari alone" viewpoint, it's just an issue of numbers. There are a lot of Junkers. While I'm sure the odd escorted transport poking through is welcomed, the sheer numbers of them using the tradelanes and/or seeking fights with the AFA/[|] sitting and minding their own business in Honshu is a bit disruptive. There's really just not that many of them and Kusari is sort of intended to be its own unique snowflake.
A concession on a topic does not mean a concession in ideology. I'm all for giving them a bit of breathing room if they're asking for it.