Simple workaround for the highlighted issues really.
Have some desiginated beam spots for each faction. I'll take the example of the GRN since that's the one I am most familiar with.
Since our main activity hotspots are Leeds/Tau-23 you could put in two faction specific warps to, say...Planet Leeds in Leeds and Battleship Guillestre in Tau-23. Additionally, a warp point to IDF should any action happen in-house. Have it cost a couple of million per jump...don't let it happen with cargo...and let it have a cooldown. Half an hour/One hour seems fine to me.
That should be able to ensure that larger interactions can take place but reduce the chance of griefing by warping everywhere at least somewhat.
That will increase the workload on people who have to implement this, but this is how I see it working. Just decide what the various major faction hotspots are, and give them warp points specifically to there.
