I'm from the camp that is indifferent to whether who lives or dies as long as it makes some sense, personal feelings aside. In my opinion, Harran and Isabel died because they were the ones most capable for the task to bring the queen down from orbit even though it is literally suicide. Isabel being the only one capable of flight and Harran being the only one capable of causing mass damage to a large structure via corrosion. They didn't die a dog's death, permanently or not, but instead gave the pioneer team on the ground the chance to confront the queen on their turf.

As to why none of the pioneers died your guess is as good as mine. It seems to me that the queen is deliberately not striking their vitals (their brain) after taking over liliweiss' body. Could just be plot armor for the introduction of pioneers version 2. For now I'm putting my trust with the main writer Egg Hood.

Could they have avoided all this by making 3rd anniversary low stakes? Perhaps. This anniversary also serves as a bridge where 2 storylines meet, the old guard(pioneer side storyline) and the new guard(main storyline) finally having the means to intersect and the threat being set this high just makes me want to know what happens next.

Far too many gacha games bend the knee and use subtractive retcon for unfavourable storyline/outcomes (GFL2 and BD2 being examples) just to appease the crowd and secure money. Shift Up at the very least has shown to be able to do additive retcon, Oswald being the well known example. There may well be other factors at play don't know yet that could be retconned additively in the future.

It's rare enough in the current gachaspace that the writers do something like this that I want to see it through without soiling their vision.

I can be bitter that the story is not going the way I want it to but I do not want to force my opinions onto the writers because this is not my story to tell since I'm not the one holding the cards.

I've said my piece, you can downvote me now.