You're missing the second half of your reasoning here. Why would Java applications be unsuitable for something CPU intensive? It matters more how you build your program than what technology you use, as long as you use the right data structures and algorithms, Java is as suitable for CPU intensive tasks as any other language.

For what it's worth, a BitTorrent client will (usually) be more limited by network and disk I/O than by your CPU, as those tend to be the bottleneck when it comes to transferring large amount of data/large amount of small packets (DHT).