Real Genius/WMG

Mitch, Chris, and Lazlo are a gender-reversed version of The Hecate Sisters.
Mitch is the maiden: he's innocent and responsible for initial inspiration. Chris is the mother: he creates things and plays a nurturing role. Lazlo is the crone: mystical and vaguely disgusting. Also, they seem to be in some sense the same person: note Chris's comment to Mitch that "I used to be you," as well as the way Sherry confuses Mitch and Lazlo.

They did something to the popcorn besides shoot it with a laser to get it to rupture the house.
Genetically altered superpopcorn? Maybe it wasn't real popcorn at all, but super-expansive foam kernels with greater force and resilience to crushing force than mere Zea mays averta. The science group may even have weakened the roof and wall seams of the house just to get the desired effect. Just because Myth Busters busted the details shown on screen, doesn't mean there couldn't be an unseen explanation!
 * If you recall, Ick had shown off genetically engineered jumbo cherries earlier in the film. Not too much of a stretch to believe that he came up with a super breed of popcorn and maybe worked with Jordan to make the optimal giant Jiffy Pop tin.
 * Concurrently, upon learning about Hathaway's aversion to popcorn, Chris had Ick create a super breed of popcorn for use in a (possible) small scale prank, and later decided to one-up the prank upon learning of Hathaway's treachery.

It was an Esoteric Happy Ending.
Hathaway's weapon worked. Blowing up Hathaway's house still proved that it worked; and it's shown that the CIA knew it was a problem with targeting; not the laser function. Chris had given the schematics (the dynamite laser) to Hathaway before he decided against it. Even if the original Kill Sat was destroyed after destroying Hathaway's house due to the reflected laser; Hathaway and his military contacts would have made copies of this information. The kids notifying the Dean and a Congressman simply meant that there was evidence that they were working against National Security. The CIA got other Kill Sats created; and the kids got expelled and/or arrested.

It was a straightforward Happy Ending.
People saw the laser fire, and one of those people was a congressman. The news media would have been attracted to a story about a house cracking open after being filled with popcorn, and eventually more facts will emerge. Thanks to this the use of a laser will be subjected to public scrutiny. Congress will hold hearings on the ethical ramifications of the usage of such devices, and at worst the project will be buried under red tape. And thanks to The Great Politics Mess-Up, the laser project won't see the light of day thanks to the end of the Cold War and the collapse of Soviet communism.

As for Chris, Mitch, and company: at worst they get a slap on the wrist for breaking into Hathaway's house. Kent becomes a more spiritual person and mellows out, thanks to his encounter with "Jesus." Chris graduates with Dr. Meredith's blessing and gets the Darlington job; Mitch graduates a few years later.

Hathaway is just about the only person who doesn't get a happy ending. He doesn't have a house, and the government audits him for the money that was spent on the laser project (which, if you recall, he instead embezzled to fix up his house). He probably will also be brought before a board at Pacific Tech, and will lose his tenure and his job.