But Spider-Man is a Marvel Character, the Justice League isn't
That's the same conditions that were present with the several Marvel/DC crossovers in the comic books, but they still made it work.
As it is, allowing the use of Spider-Man benefits them. There is no benefit to the MCU in using the Justice League.
Certainly there is. The comic book superhero franchise is booming right now, whether those characters belong to Marvel, DC, some other publisher, or are simply original characters. Granted, not every movie is a blockbuster, but they all attract their audience, and they have all managed to turn a profit. It's like all of the other movie trends before. Not every Western was "Shane," High Noon," or "Rio Bravo," but they all made their contribution to keeping the genre going and keeping the fans interested for decades. Superhero movies aren't going to be this popular forever (frankly, I doubt that they will last more than another 5 years, tops) but, while they are, any chance to make a profit on a movie is most likely going to be taken. I can't see very many fans of either DC or Marvel boycotting the movies, just because the other group has infringed on their favorites.
They would spend hundreds of millions of dollars for a movie that has no stake and would not be tied anyway into the current storylines.
So, it would be a stand alone movie. Hollywood makes them all the time. That, or some screen writers would come up with a way to actually tie them together, the same way that MCU will supposedly be incorporating the Fantastic Four and the X Men into their universe within the next few years. The Watchmen aren't supposed to exist within the regular DCCU, either, but Dr Manhattan was used a few tears ago to straighten out some of the mistakes that the "New 52" reboot of all the DC characters had caused. If there's a way that seems even slightly likely, and someone in Hollywood can make a strong enough pitch, I have no doubt that the movie, or some variation on the idea, like, maybe, a Batman/Captain America team up, will happen.