For example, there has been a lot of speculation about potentially one day seeing an adaptation of the 2008 comic book crossover arc Secret Invasion, and there is nothing in Captain Marvel that disrupts the idea of that happening one day.
So while the end of the blockbuster has Carol Danvers supporting a group that definitely deserves help, you shouldn’t count out the possibility that we still could see some nefarious Skrull plots play out in the future of the Marvel Cinematic Universe.
There is also the fact that the Fantastic Four will soon be a part of the franchise, thanks to the still-developing Disney-Fox merger, and that is a team that has done a whole lot of clashing with the Skrulls over the last 60 years (including fights with the Super-Skrull, who is a Skrull imbued with the powers of all the members of the Fantastic Four).