If you set your scanning priority to low it will only use 1 core of your CPU for scanning. You need to set it one higher, to "Below Normal" for a real time benefit. On my PC that means: Low = around 8 hrs for full scan, Below Normal = 1,5hrs for the same full scan. I've got a quad core machine.
Don't forget, even if the CPU get's hammered, the priority is still lower of all the other tasks, so the open programs won't suffer from lower performance.
The main problem is anyway the harddrive. We have here now in most computers an SSD as main drive and the users don't feel any performance degration while scanning. On the other hand, the few people with a traditional HDD can barely work because the harddrive is so slow.