I doubt that all the aliens that were encountered were entirely benevolent. I am sure some of them did, in fact, work with the syndicate. At least, I hope that is revealed in time.
The key falsehood "My Struggle" proposes seems to be that the syndicate orchestrated the invasion, allowed Mulder to think it was happening ("The Truth"), in order to subdue his quest for the truth. That truth being that the syndicate, or whomever was in charge after the original group was killed, had designs on using alien technology to institute their own nefarious take over of the world.
This solves two problems. First it dances around the issue of the December 21st, 2012 invasion date that was previously set in stone. It's now more of a soft launch for whatever the shadow government is planning. Second, it allows Chris Carter to adapt the show to the current post-September 11th sociopolitical environment that is fearful of government spying, corruption and war-mongering in a way it never was before.
Carter was a bit clumsy in the execution, and he needed a two hour premiere, but I think the episode does solve the above problems. The show is now designed to play on current fears but without dismissing its supernatural roots. It's a very well thought out design.