^Simple, the Skrulls have nowhere else to go. Their religious beliefs told them that Earth belonged to them. They were and still are desperate.
The outcome is that we now have several thousand Skrull prisoners on Earth, Stark is out of a job and is now the world's most wanted man, Norman Osborn is the most powerful man in the world's superhuman community, Ms. Marvel wants him dead, the Inhumans are going to war with Emperor Vulcan and Shi'ar and oh yes, Osborn, Dr. Doom, Namor, Emma Frost and Loki are now running the show.
While I'm not going to call for the predictable, one wonders who will betray who and how it will happen with the DI. Their greater goals may be tempting, but these are by and large not trustworthy folk. Loki and Doom are the most obvious, but they're almost too much so. Emma may have the idea of betraying the others to increase the public standing of mutants. The Hood may want nothing more than to keep things even for the street-level criminals and to keep anyone other than Dormammu from conquering things. I'd put my money on Namor having the best exit plan, and if Poseidon is behind him, he'd have less to fear from Loki and Dormammu.
I'm going to guess that the DI will run more smoothly than the LI on the surface, but watch out below.