The context of their "violence" ultimately depends on the perspective from which you judge their actions.
Yes, in the context of the wishes/desires of the present characters, they do seem antagonistic and foes meant to be overcome.
But, we know there's more to their presence and purpose. They are protecting a "fate" that we know the conclusion to, and that the characters themselves fought to make happen. It makes sense that the Planet would protect it, given the fact it's the future that allowed it's sustained survival. Not only that, but the spirits of that future would wish to maintain their own existence.
And the same can be said about the sentiments of fans wishing to protect the story and it's direction.
That's the conflict and question that's meant to be elicited with this choice and dilemma. I think it's an interesting examination of how one approaches revisiting this world, and what the consequences of "remaking" could be, diegetically and in reality. On one hand, letting the characters fight for themselves in the present creates the risk of throwing off the guardrails of destiny that ultimately led to the satisfying and positive conclusion to the saga of FFVII that the Planet itself wished to avoid. And honestly, what the character's future selves wanted.
However, hope and the inherent struggle to survive and enjoy fleeting moments of life makes one want to see these moments again. Do things over again. Try to find a better way. However.... I think it's telling that Sephiroth most of all seems to want to do this all again, all to avoid a "destiny" which will prevent FFVII from ever meeting it's end. Every wish comes with a price, and what that price is, remains to be seen.
So yeah, I think the meta commentary is a bit too heavyhanded to ignore or assume coincidental. However, I definitely don't think it's malicious. It's only malicious from a limited view or analysis of the context.
