Honestly, yeah that would have been cleaner. Would it still get reader backlash? Of course it would. But as you said, it would be cleaner, and they had a
perfect excuse for it. Secret Wars is happening, there are multiple realities and versions of everyone running around. Reality is in flux.
The timing for this arc was completely out of sorts. It's running parallel to Secret Wars, anything that happens in it literally does not matter because the incursions already happened, and everything can change again.
Hell, if
Renew Your Vows gets super traction and sales, maybe that'll be the new reality when SW finishes. Since Miles Morales is taking the Spiderman mantle, at least partially, that gives Parker the breathing room to have a family, and if fans show through sales that's what they want, that can happen.
Of course the twins' new origins
isn't something we want, but at least the explanation would be simpler.
There's been subtle changes to the timeline already. In
Rage of Ultron (which is set post-SW, and also written by Remender) for example, there's a flashback scene at first showing the classic Avengers team (original costumes, Beast being part of the roster and in his original classic form, Pym in his Yellow Jacket phase etc.) fighting Ultron. In the old comics from this period, I know that Wanda a) couldn't fly and b) didn't have very good chaos abilities yet. However, this fight shows her being able to fly, and also being good enough with her chaos warp to hold Ultron for a bit. Subtly, this retcons her into having stronger chaos abilities beginning from the Silver Age, instead of it happening later. This really works fine, if the retcons happen like this, I'm okay with it.
Granted, a new origin is a totally different level of impact, but still, you have a retcon event happening, Marvel should just
use it.
Edit: The scene from Rage of Ultron I'm referring to