I assume they'd have no issue. There was that talk going around that Marvel didn't want anyone creating new mutants because their rights automatically go to Fox. I'd assume the same goes for Sony's Spider-Man rights. It's still up in the air, but I don't think Sony has rights to Spider-Woman. She's a part of the Spider-Verse team-up, but her origin and much of her history doesn't tie into that part of Marvel. The idea of clones and multiverses might be a bit too convoluted and, frankly, dumb for cinematic purposes though.
Well, what I'm suggesting isn't using that story so much as using the concept of a Gwen Spider-Woman presented there and applying it to the Clone Saga narrative. And, I'd argue the clones were only convoluted in the 90s because the writers let it get convoluted, with the whole drama of who's the real Spider-Man and whatnot, which is why I suggest completely ignoring Ben Reilly.
Just have Kaine be a messy attempt by Oscorp to create a new Spider-Man for their purposes, and then have Miles Warren create a better one modeled after Gwen because he obsessed over her when she worked there. Peter encounters Gwen, and it creates tension for him because by then he's dating MJ. Then, Kaine shows up while Spidey's patrolling the streets and chases him down. Eventually, the plot leads him to Warren, who reveals the program to recreate Spider-Man and in some capacity becomes the Jackal. In the end, the Jackal is defeated, Peter and MJ come to grips with the Gwen situation and are closer as a result, and Kaine and Gwen are seen moving to Texas, perhaps already designing their new costumes.
Boom. I would love the heck out of that movie.
(Of course, Sony probably doesn't have those rights, but oh well. A fellow can dream, right?)