In this case it doesn't seem like much of a conflict. I think that barring more-or-less obvious signs of disarray we can count on organizations trying to serve their leaders' self-perceived interests - which, while evil, entail not killing humanity - unless and until the singularity changes the game.
we can count on organizations trying to serve their leaders' self-perceived interests
James Q. Wilson wrote a book explaining why this often isn't so.
You might also consider looking a Essence of Decision, which analyzes problems JFK had trying to control various government organizations during the Cuban Missile Crisis. If you want to say that the relevant leaders were the heads of those organizations (eg. the Secretaries of State and Defense), you need to articulate a non-circular theory to identify who the leader of an organization is.
If I understand the Singularitarian argument espoused by many members of this community (eg. Muehlhauser and Salamon), it goes something like this:
I'm in danger of getting into politics. Since I understand that political arguments are not welcome here, I will refer to these potentially unfriendly human intelligences broadly as organizations.
Smart organizations
By "organization" I mean something commonplace, with a twist. It's commonplace because I'm talking about a bunch of people coordinated somehow. The twist is that I want to include the information technology infrastructure used by that bunch of people within the extension of "organization".
Do organizations have intelligence? I think so. Here's some of the reasons why:
I talked with Mr. Muehlhauser about this specifically. I gather that at least at the time he thought human organizations should not be counted as intelligences (or at least as intelligences with the potential to become superintelligences) because they are not as versatile as human beings.
...and then...
I think that Muehlhauser is slightly mistaken on a few subtle but important points. I'm going to assert my position on them without much argument because I think they are fairly sensible, but if any reader disagrees I will try to defend them in the comments.
Mean organizations
* My preferred standard of rationality is communicative rationality, a Habermasian ideal of a rationality aimed at consensus through principled communication. As a consequence, when I believe a position to be rational, I believe that it is possible and desirable to convince other rational agents of it.