Even running at a few %, modern processors are able to keep a disk pretty busy.
A couple of ideas perhaps
1. Run it as an "idle" process, so it only runs when there is definitely nothing else going on.
2. Run it as a screen saver, so it only runs when you're not using the machine.
3. Run it overnight, when you're not there at all.
4. Buy a second hard disk, which is used exclusively for your intensive program. Even better if you happen to have a dual-core machine to begin with.