What purpose did the isle Azys La serve? Main Storyline Spoiler.

[Delily]

I think you are mistaking the implication and the point of the story. Technology and knowledge itself is not evil. It's a tool. How you use it is how it is defined. There is nothing wrong with rediscovering what Allag achieved. The point the game has made so far was not that "tech is bad, but do it anyway," but "This is what we built, but we lost sight of what was important. Instead of tech supplementing our lives, we grew dependent. Instead of living on this planet, we attempted domininance. Continue to grow, to learn what we learned, to achieve what we achieved, but now know how we failed so you can spare yourself our fate and surpass us one day."

Binding primals to use as an aetheric source of energy constitutes as a Really Bad Idea. Not only do you make them upset in the event they are freed, they represent a constant drain on Hydalyen.
Making pacts with a voidsent is also a Really Bad Idea. Allag was also involved in bioengineering. If anything, the lessons to be learned are to avoid doing what the empire did.