ばか！バカ！　馬鹿ー月！

If you've just read the last little update (34%), you'll see that at the end, the president pulls out a cigarette and tells Koizumi that speaking in that serious voice is irritating. This my description skips out on a few details so go read it.
Anyways, this is implying that the President and Koizumi are fellow workers for the agency. So I'm guessing that this is all a ploy to keep Haruhi further entertained (as you can see she seems very bored in the beginning of the novel). Also, we see Kimidori on the scene, I believe that this is the first time we've seen the Data Aliens and the Agency work together outside of the SOS Dan. Is there something else behind this allegiance, or is it just that Kimidori is part of the Agency. But if she was, why was Yuki transferring data from Kimidori (I'm guessing that that was the purpose of the stare off).

I got the impression that Kimidori was the driving force behind what was happening and that the President, be he member of the agency or not, is playing along.

Why? I guess we'll find out soon enough.

From what I could read from the text, I think Kyon and Koizumi discuss this and she was apparently in the student council before they had the guy become the president. My ability to read is very poor but I'm pretty sure that Koizumi says that she isn't working for them.

Well, it's too early to spoil things now, but all I can say is read chapter 2 of volume 7 right after it's translated. Are the aliens and the organization working together? Or are the aliens in the same boat as the time travellers? Only time will tell.... XD