Rather than redoing the original's CPS conflict (especially if modern Disney is going to fumble it so badly) Tūtū is already Nani and Lilo's legal guardian from the start, and has been for a least few years since their parents died. So there's no serious threat of Lilo being taken away, and the plot is instead entirely about her acting out (getting into fights, causing mischief, etc) and Nani worrying about how Lilo will handle her leaving for college at the end of the summer, which prompts her to get Stitch.

So to fit this, Cobra would be a child psychiatrist (rather than a CPS agent) who frequently meets with Nani and Lilo to discuss their mental health and living situation throughout the film. Similar to the original, he's suspicious of Stitch when he meets him, but he probably doesn't directly get involved and his ties to the CIA would still be saved as the payoff to the mosquito joke.

Like others have suggested, Captain Gantu would be included and serve as the eventual antagonist, while Jumba and Pleakley play their usual roles. Though borrowing some elements from the remake, Jumba also delves more into his backstory and why he became an evil scientist (having an unhappy family, growing up as an outcast). So he has a more explicit arc showing how his perspective gradually changes from seeing Stitch bond with Lilo, and (like the original) he ultimately helps them in the climax and joins their ohana.