I have mixed feelings about Pietro when it comes to his relationship with Magneto because of course what Magneto did at the end of HoM was unnaceptable, despite the cricunstances but for me a comic book fan who read about Magneto and Pietro relationship in the 90´s this moment was as occ as Magneto´s and Lorna´s fight during Trial of Magneto, the main difference being that HoM moment was a little better written than Lorna and Magneto´s fight.
That said I think I can add a little into what exactly Magneto meant with the "You used me" from Bendis original story. At the time of HoM, there was subplot over Excalibur title by Claremont in which it was explained Wanda and Magneto´s powers merged during her treatment at Genosha, her power represented the possibilities, what could be, while Magneto´s powers represented what it is, the physical world, which made her powers more real and more able to manifest on a greater range but also harder for her or Xavier to control. The life force was not yet part of the story, so to create HoM Wanda didn´t just use her own powers, she used also Magneto´s energy and Professor X telepathy to change everybodys memories but also subscounsiouly gave or awakened Layla Miller´s powers because a part of her didn´t agree with what they were doing. So when Magneto talked about Pietro using him and Wanda he was talking about at the time.
Now on Pietro´s and Magneto´s relationship in the 90´s was a lot closer and you could even argue he was his only confirmed child as far as marvel was concerned or at least the one closer to him because Wanda spend her time over avengers titles with the sole exception of Dark Seduction. At the time, Magneto asked Amelia Vogh to protect Pietro during his attack on earth during the War of Magneto story and after that during Pietro´s stay on Genosha, he even named Pietro´s one of Genosha´s diplomatics to the UN a role that Pietro took seriously.
Magneto didn´t have strong feelings Pietro would ever see things his way and during Dark Seduction he saw Pietro bringing the avengers to Genosha more like his Son bringing his annoying friends to the country than a betrayal and he expected Wanda, Pietro and Lorna to oppose him getting his full powers back as well, in fact he talked about him using this opportunity to bring back his powers as his last chance to reconcile with his children and he did it still for, in his mind at the time, the chance of a mutant nation. So Magneto very much was used to be the villain in his children´s stories and this was referenced later by Bendis on HoM, when Magneto sees his decision on DS as a prologue to choosing mutankind over his family and losing both anyway because Genosha was still destroyed, this is also referenced by Pietro during his talk with Wanda, it wasn´t Ultimate universe being referenced, it was that moment.
Pietro and Magneto relationship was not good, you could call it more like a chessgame between them in which the other one is always expecting the other shoe to drop but they still cared for their mutual well being, still their relationship was way better than HoM and posterior stories suggested, I don´t see that Magneto killing Pietro. So I agree marvel writers often don´t consider how damaging their stories can be to the characters relationships going forwards but more so in this case where they don´t even try to fix some of the damage and that´s a shame. I don´t think we can have a more genuine Magneto´s family story if the writer doesn´t addresses all of this instead of adding more to the damage, like Leah did with Lorna and Magneto.
After Trial of Magneto if marvel say Magneto´s family will never meet again, I would believe them because this is how broken things are between the characters, so much that even Wanda and Magneto´s hug feels empty because there has not been a story leading to it. I liked Wanda and Magneto´s hug and I guess Issue #5 will explain a little more what´s going on but I can´t enjoy it fully after all the occ moments we have seen from Magneto and the other characters so I hope at least this gives us an end to the decimation issue because it sure doesn´t works as a magneto family story or even as a magneto trial story. So I hope it at least gets to undo the decimation issue.