The problem is that you can't (and shouldn't) tell other players how to play the game. It's a game to be enjoyed. MS isn't a problem there, as they are playing the game in a way they enjoy.
However
I also see what the loyalist units are trying to do, which also makes sense. They are trying to give their faction direction, and a lot of players like having direction to their actions. They also try to set up aggression and alliances to better the game play for their faction.
One example: Marik and Liao have a cease fire. Each side respects it. This is not to hinder game play, but is instead to help Liao fight Davion, as they seem to have a low population. This prevents Liao from being rolled to their Capital and effectively being killed off. This permits Marik to also shift players from attacking Liao to some other front, such as Davion (whom at the time had a very large population), thus placing more pressure on Davion creating better fights overall.
Each side is correct in their way of playing it. I do agree with the loyalist units that controlling the engagement zones can increase not just the feel of the game but also give units direction and focus. We can't tell MS how to play, but I do believe that units such as MS should at least consider the goals of the faction they join and be respectful of them.
This is a tough one to make any judgements, and if MS really is just joining into a faction to purposefully break their alliances, then that I would say is wrong. If they are just joining into a faction to attack whomever they feel like (not caring if there are alliances/not intending to break an alliance because they don't know/care about it), then I see no problems. As we can't gauge the units intents behind their attacks.
Until PGI decides to change something as an interaction tool between loyalist units/players and mercs/non-loyalist contracts, there is nothing we can do but ask that they preform certain actions. If they don't adhere to the request, then we must leave them be as there is nothing we can do about it and we can't go telling everyone else how to play their game either.
Also, do recall that CW is in Beta still. The map will most likely be rest (my guess) once they have the system more cemented down, especially if we still have wormholes all over the place...