Top500 computers could have done this sort of attack when CPU and/or GPU mining was all the hype, but now with FPGAs and ASICs, the hardware required to have an impact is too specialized for any sort of general-purpose computing.
The global network hash rate is currently 35 Thash/s.
A typical GPU found in a supercomputer (Nvidia Tesla K10/K20/C20xx) does roughly 100-200 Mhash/s.
A typical modern CPU core does roughly 1-2 Mhash/s.
You would either need 175k-350k GPUs, or 17.5M-35M CPU cores to attack Bitcoin. If you look at the Top500 list, they have maybe a few tens of thousands of GPUs combined, and about 10M CPU cores (watch out, the core counts in the list combines CPUs and GPUs, I found this out when making sense of the numbers years ago: http://blog.zorinaq.com/?e=14 )
Plus the network hash rate is predicted to increase by at least +20 Thash/s (to 55 Thash/s total) in the next month due to Avalon finishing delivery of their first batch of ASICs. Bottom line, no, all Top500 computers combined could not attack Bitcoin.
(Just curious)