Let's see. We've seen what happens when creation is reversed and the results weren't pretty. An entire race turned into divine flesh. Not divine beings, just divine flesh.
?
First, what the Altmer wan't to do is entirely different from what the Dwemer did. Second, who says the dwemer aren't pleased with what happened to them? They became 99% of the best entity in all of the Arubis. Sure, they're missing a pilot, but besides that, all is well (or, well, all was well before it kept getting destroyed). Some of my best friends would love to upload their souls into giant stompy robots (they're transhumanists). But what the Altmer wan't to do is entirely different. They want to get rid of death and all physical limitations, plus free up time.
I have to admit, the phenomenon of evil golden Nazis just sits a little bad with me, as far as ambiguous Elder Scrolls awesome storytelling goes, particularly as it has gained more attention with the Thalmor. ES has made its bones off of letting things be grey; people trying to categorize the Daedra as "demons" on the forums have always had to come to grips with the reality that nothing is that black-and-white (or just clear, one-sided, and blandly coherent) in this world we love.
To play the 'invading, insidious racists that we can all uniformly hate' card is a tad too obvious for ES' standards.
Here's the thing: the Altmer are total monsters in our world, where all races are equal, getting rid of the laws of physics would just kill everyone, and things make sense. But they don't live in our world. They occupy a moral grey area in a world where, basically, every race but them has a horrible heriditery illness that cuts their lifespan dramatically, and reality is just a horrible cage. Now, I won't claim that they're seriously "on the right, 100%", and clearly they're going about things in basically the most horrible way possible, but I think part of the fun of fantasy is how changing a few factors of the world really changes how you have to look at everything. Maybe its just because of all those "critical reading" lessons they drilled into my head in middle school, but I'm naturally inclined to look at any group being portrayed as villains and try to see how they might be heroes. I think its really fun, and I think maybe you should give it a try.