Oh, of course you can have more than one version of Spider-Man running around. That's what we have now. Not to mention more than one Spider-Woman. However, there are a couple of things we have to take into consideration.
Miles being front and center on this cover is a huge statement by Marvel. It not only suggests that elements of the Ultimate Universe will remain and be part of the new Marvel Universe post-Secret Wars, but that Miles, not Peter, will be
the Spider-Man of the new Marvel Universe. After all, notice which Spider-Man is being predominately featured in all the Secret Wars promos? It's Miles. Whose the most popular character from the Ultimate Comics line who also has a fanbase of his own? Miles again. Who is a closer fit Marvel's vision that Spider-Man should be about youth? Again, it's Miles. And we're getting an Amazing Spider-Man story during Secret Wars showing us a married Peter Parker and Mary Jane with a kid,
in which Dan Slott has said will be a "monkey paw" scenario in which "No matter who or what or how Spider-Man comics will be made in the future—elements from this story will go on into the next incarnation.” Also, within the past four years, Marvel has had
two successful Spider-Man comics in which Peter wasn't the lead. First with Miles after the "Death of Spider-Man" event in the Ultimate Comics, then with Doc Ock taking over Peter's body in Superior Spider-Man. Wouldn't surprise me in the least that what Marvel took from this and the response towards both--each which received mainstream media attention--is that Spider-Man does not have to be Peter Parker to be successful.
Thus, we potentially have a situation in which Marvel can have their cake and eat it too--that they restore the marriage (and throw Peter having a kid for good measure) that thus retcons the still controversial One More Day, while also getting back a younger, teenage Spider-Man via Miles which, as an added bonus, is more reflective of contemporary youth culture. And, under this scenario, Peter would still be around, just not active as Spider-Man, mentoring Miles and also supplying him with web-fluid and other gadgets.