We just have way to less information for that. Maybe it was in the will of the ones that summoned her that wanted the shattering because they saw that how powerful their race is, its too dangerous? We just know the view of those that summoned Zodiark, those that were ready to sacrifice big amounts of their own race so that he can solve their problems. We also know that only one member (probably us) was against his summoning but at the end Hydaelyn had so many followers that she somehow was as strong as Zodiark (and he somehow lost one halo) and was able to defeat him. So even if Emet goes around and sees himself as the right one, they choose sacrifice as their way to end the conflict (but dont accept the sacrifice and kinda are living in the past just like Nidhogg did) while others saw that this was wrong, especially since they wanted to kill the new generation (which were still with complete souls!) just to get their old ones back..I doubt that those who summoned Hydaelyn did this with the same view and belief than those who summoned Zodiark.
Hydaelyn herself probably did not tell the whole truth (she only did lie about who came first, she was telling the truth about Zodiark threating life since he should get all the new souls as sacrifice) because she needed us and maybe was afraid that we would listen to the Ascians. We have people like Urianger that lied more than once to get to his end and yet he is no bad guy. Hydealyn lied to us once, otherwise her actions are good. Why should one action destroy the rest of it?
The Ascians and Emet in turn have done more bad than good to us and seemingly even went against the wishes of some of their own race. I feel bad for him but he was wrong and like the OP stated, alot of the conflict only was started thanks to them and seemingly their race was not even that great either since Zodiark only was summoned when their city was under attack..they seemingly still just discussed helping the rest of the cities when those were also under attack..so Alphinaud is quite right, there is not much difference between us.
What if she simply does not know their whole motives? She was summoned as the enemy of Zodiark and those that follow him. We dont know if she even knows why that was the case. Maybe she even got told the story wrongly. In the end she did not tell us the full truth but the Ascians themselves proved that they could not be allowed to live. I mean why is it bad to kill them off? These guys have for thousands of years tried to rejoin the shard, made one shard into the void and succeeded with a couple of rejoining too which killed billions of people and other life..but Hydealyn wanting to take them out is bad? No matter what happens to them, their plans (even worse now that they even want to sacrifice the source people too) are so bad that we can never allow them to happen, so why should she care..at the same time she never went to us and said: Kill those guys, only after new conflict arised with them did she try to tell us more. Otherwise she mostly left us to our own devise, told us to "feel, think, hear" for ourself" and used her all to defend us from certain death. And as others pointed out we see her view in "answers" and she does not force anyone to pray to her, heck most people dont even know she exists..You completely ignore all the good she had done and accuse her of being evil just because she once told us a different version of the story..while completely ignoring that we also only saw the view of the Ascians who claim to be tempered to Zodiark..and ignoring that we already have people from their race who were against them too..heck it was their own race that summoned Hydealyn.
Why does man need to kill her to have their own history? Our history only was ever possible thanks to her. Us not being rejoined and destroyed was only thanks to her and her WoL..its funny when man wants history without a god/primal but only lives thanks to that. And Hydealyn mostly even leaves us to ourselves. She only saves a small few like us or Kryle. In times of peace or rebuilt between the calamities she is not that active either. Heck barely anyone even knows that she exits..so without Ascians trying to stir things up, man already has the reign over their history.
Yes he knows it from the beginning that we are at least from his race and at the end he even for a short time sees that we may have been even a close friend of his but does not want to believe that. So here we have another Ascian that is not outright telling us the truth. Not only that he knew about our soul but does not truly say it (just these small hints) but he was ready for us to become monsters if we dont win the test. Heck I wonder if he ever believed that we would be able to do it. He was angry that we destroyed his plan but seemingly got a new one, so I think he hoped that we would get all the light and then turn into the worst of the lightwardens..killing us with that and starting the rejoining again.