Narratively, Powerplay agents are working on off-the-books deniable tasks, so taking out the agents doing the same for the other Power is fair play, regardless of how much your respective leaders smile politely and shake hands and pretend everything is fine for the press - and "you shot our saboteurs" isn't going to get raised as a formal complaint, so that's all good.
In-game this doesn't really come across - in the same way that there's a contacts link for the Black Market where you say "I want to sell illegal goods" and it isn't just bait for the least awake members of the criminal underworld ... and the various concourse mission givers stand around shouting "Hey, any murderers around here? Looking to hire a murderer!" ... and so on. You just have to pretend everyone (including you) is being way more subtle than they are shown as, and all the prep work where you discover that a secret Mahon weapons convoy will be passing through this system at a particular time using these fake IDs happens off-screen while you're logged out, so your in-game time is then just the bit where you shoot them down and leave the scene before anyone notices.
In-game this doesn't really come across - in the same way that there's a contacts link for the Black Market where you say "I want to sell illegal goods" and it isn't just bait for the least awake members of the criminal underworld ... and the various concourse mission givers stand around shouting "Hey, any murderers around here? Looking to hire a murderer!" ... and so on. You just have to pretend everyone (including you) is being way more subtle than they are shown as, and all the prep work where you discover that a secret Mahon weapons convoy will be passing through this system at a particular time using these fake IDs happens off-screen while you're logged out, so your in-game time is then just the bit where you shoot them down and leave the scene before anyone notices.