Same problem any Avengers film has. You solve it by giving everyone a specific task tailored to their skillset and powers; Carol punches the Big Bad (Kree Sentry, Super Skrull, whoever) while Kamala fights the minions and saves innocent bystanders, and Monica disrupts the doomsday cosmic machine thingy. Easy enough.
There's plenty of things you can use as a physical threat for Carol; Sentries, Super Skrulls, Korvac, Adam Warlock, that Summers brother who's name I forget. Celestials, maybe the Shi'ar and/or Eternals. Hell just bring back Annette Bening as the Mar-Vell from the Cancerverse (use the nega bands for a powerup, if being an immortal necro-thing isn't enough of a boost).
And Carol's pretty easy to challenge even if you can't punch as hard as her; attack on multiple fronts, use an endless horde of minions, use innocents (like Sutekh suggested), manipulation and lies, psychic attacks, go after her loved ones.....lots of ways to get around her powers and hurt her.
But I think with Carol, her story really isn't about the external threat at all. I mean, the villains in the MCU are all just reflections of the hero's inner struggle anyway, but with Carol it really is *all* about her own internal dialogue and overcoming her own demons; beating up the bad guy is just the victory lap she takes after getting over her issues.
This is where I think they're going with her; the Kree/Skrull situation will prove to not be as clean-cut as she thought, forcing her to question her actions and wonder how badly she screwed things up and how many innocent people died because of her. Both factions have some heavy hitters that can take a punch from Captain Marvel, both have ways to challenge her beyond raw physical ability, and the conflict between the two races can become extremely muddled to the point where there isn't a "good" side and a "bad" side, which makes deciding who to punch harder.
Huh. Wonder if we'll see her start drinking?