You are right that supercomputers are designed to do parallel computations and are not general purpose computers. They are great for bitcoin mining, but they are still far too weak to present a threat.

We don't have to try to convert petaflops to hash rates. Let's assume best case here. nVidia GPUs are not suitable for mining bitcoins but what if the GPUs were AMD 7970's instead? Then, 18688 AMD 7970's would have a total hash rate of about 18688*650 Mh/s or about 12 Th/s.

The total network is about 180 Th/s, so this super computer with only 12 Th/s is still not nearly enough to mount a 51% attack.