I am not going to say I believe that SV is a company with great forethought behind their changes and or game mechanics...
BUT I do think they have a broad set of ideas for the game, and what they are attempting to do with the game mechanics that are in the game is that being a player of "low" reputation forces you to play the game with less options, you are not protected, you do not have by default safe places to go back to, you are an unwanted person in the "safe" areas of the game, BUT that is only for the "kingdom" in question that you have this "low" standing for yourself, that means you can choose to go else where and try to keep your reputation there instead.
Now if you are purposely performing in-game functions that cause rep-loss like I do, then you need to accept your fate regardless of how it occurs, I play with people whom in most cases have also chosen not to use the "safe" areas of the game, we work together to farm resources, to protect resources, to get foot hold on areas we desire, and with that we fight in those locations to prevent other players from getting resources we have already farmed or to limit the availability of those resources.
There will be a lot of people who will dislike that, and that is OK, this is the way we play the game, and if you want to stop us from playing the game this way, I suggest you find like-minded people to play with, get resources for equipment, and kill us at those locations as a group. Otherwise you would be more productive to go to the feedback/suggestion area and ask for mechanic changes with a poll, because it just sounds like you want the GM's/Developers to change the game to fit a view that is not currently in line with the in-game features/functions.