In Dawnguard, however, i think there is an explination.
First, we are told, quite plainly, that the Dwemer of Skyrim (at least, possibly even Morrowind, though those cities would have been united under Dumac) were organized into a series of City States, similar to ancient greece, which would men the potential for radically different cultural practices and temperment between, say, Markarth and Mzulft.
Second, we are told by Gelebor that the Falmer were not, in fact, tricked, but expressly told they would have to blind themselves if they sought refuge amongst teh Dwemer cities. This is extreme, though understandable, because the Dwemer have always been prone to keeping secrets. Gelebor also indicates that this blinding could not explain what the Falmer became.
We also know (or at least are told in one book...) that the Dwemer enslaved the blinded Falmer, which could explain their further decline into xenophobia. We also know that, supposedly, the greatest volume of their population is in Blackreach, which seems to be the primary source of Aetherium.
Which brings me to my point, and my newest explination for the differance in the actions of the Skyrim Dwemer. Aetherium, the obsession with it, the desire to utilise it, and the war over it explains not only why the Falmer were enslaved, presumably after the initial pact, but could also explain both their insanity, and the seemingly dark madness of Skyrim's Dwemer. We know next to nothing about Aetherium, really, only that its a minor curiosity to most of Tamriel, and that the Dwemer of Skyrim found a way to refine and forge it. Then they went absolutely crazy over it, fought a series of internicine wars, and were largely beaten by the Nords afterwards.
If they were willing to butcher eachother over Aetherium, then it's easy to see them violating their own pact with the Falmer and enslaving their blind cousins to mine the mineral. As their obsession grew, so did their misstreatment of the Falmer, leading to the development of all those lovely torture devices we see in Dwemer ruins now.
Does that make sense to anyone else? Does the inclusion of the Aetherium lore sufficiently explain the change in the Dwemer, without invalidating earlier information, or am i grasping at straws here?