I'd suggest that for the purposes of players trading or even trade factions, both parties have a reason to maintain it. Getting supplies from your allies enemies is nothing new and whilst it might cause 'some' concern, as long as all parties attempt to keep it quiet or at least not wave it in your face, I can't help but think it's really on the level.
Military action is however something entirely different. It's not something that can be easily explained/hidden.
From 'The supply ship was hauling badly needed medical supplies' to 'Yes it was us. We blew it up' have a hugely differing affect on your allies.
That kind of thing might happen once and people get yelled at/fired/shot. Happens twice and then things I would imagine would be a whole lot harder to get away with.
Diplomacy is very messed up and it has very little to do with vanilla lore, either way. It's definitely who you know in skype and not what your badge says.