Wow this is an old thread.
As for your question aRaSamy, without downloading your manual, I would have to say that with the JMicron controller disabled, the IDE controller will be disabled. Intel dropped support for IDE around the 975X chipset if I remember correctly. So motherboard manufacturers who wanted to add support were left with using third party controllers. Many used the controller from JMicron as it added additional SATA ports as well as an IDE port. I don't think you can selectively disable only the SATA, the entire controller is either enabled or not. There are a couple of ways to attack your problem. Obviously the noise created by the JMicron controller is dirtying your audio signal. You didn't specify whether you are using digital out or analog out, but for the time being I will assume analog. First off you could have a faulty ground to your speakers, coupled with extra noise from the controller causes the noise your hearing. If you think this could be a possibility, try/borrow another set of speakers to see if that eliminates the problem. If you are convinced your speakers aren't part of the problem, the other options available are:
1. Get a SATA optical drive, they are cheap, and replace the IDE HDD with an SATA drive.
2. Buy a PCI-IDE controller card. This should remove the noise of the controller from the motherboard thereby eliminating the noise you are hearing while still being able to use your IDE devices.
Hope that helps.