The way 4e's action resolution mechanics - especially but not only incombat - leverage the traditional party dynamic of D&D is, in my view, a huge strength.
But I don't think it's a strength of the game that it seems fairly easy to permit intraparty conflicts to open up, but can't easily accomodate them within its basic framework of play. (This is more true of combat than non-combat, I should add. DMG2 has a nice example of how to structure a certain type of skill challenge to accomodate at least a low level of intraparty conflict.)
And there definitely are rules systems that can handle intra-party conflict better. I know Sorcerer by reputation rather than first-hand, but I believe it can handle it well. And Burning Wheel has the Duel of Wits mechanic for handling some intra-party conflict.
If we look at 4e from the often accused perspective of it being a "supers game", inter-party conflict is quite common, especially out of combat. In combat Superman, Batman, Wonder Woman, they all work like a finely tuned machine. Out of party Batman is practicing ways to kill everyone, Wonder Woman is an international ambassador for the Man Haters Island, Superman is an alien who spends half his time lying to the world. Lets not even get started on the Green Space Cop with a penchant for breaking the inter-galactic rules or the dozen or so murderous mercenaries who suddenly decided to be heroes and think that somehow magically exempts them from the law.
In combat, these often contrary views, desires and attitudes of the heroes are ignored because there is a focus on a larger goal, ya know, like Darksied is attacking or some sort of alien-space virus is turning normal joes into murderous zombies.
Out of combat these little issues become magnified because the heroes have nothing else to focus on. Why is Batman thinking up ways to kill everyone? Why is Wonder Woman so supportive of such an anti-men organization? Who does the Green Lantern really hold allegiance to, if the Corps told him Earth was a threat would he attack it or defend it? Should Arsenal be taken to court for all the horribly illegal things he does? Hell the League has gone to blows with each other over these things when they suddenly come out of the closet.
I don't really know if we
need mechanics for that sort of stuff because honestly I think it can all be handled with good RP and thorough character development. We should endeavor to make sure our players aren't afraid of inter-party confrontation, it's good, it's healthy, even if, like the comic book heroes, there's really never any resolution.