Litecoin also can be mined by GPU. So if the government uses supercomputer, ordinary people use a bunch of GPUs can beat them. So don't worry, everything is under control.
What's your definition of "supercomputer"? I'm pretty sure a 'government supercomputer' by todays standards could out run a good few thousand consumer GPU's. If not- they would just build one that could. Or better yet, if destroying our funny money coin was really a priority, they would just build an ASIC for litecoin and wipe it out in an instant. Or if they wanted to keep the option open to wipe out any future coins as well, they might just use 50,000 FPGA's, wipe out litecoin, reprogram them and use them for something else. All in a days work at the CIA I'd say. Piece of cake.