I have Windows 8 Enterprise 64 bit.

Whenever I install or uninstall a program the Disk utilization goes to 100% and I can't do anything else while it's at 100%

Usually it's either Microsoft Windows Search Indexer or Microsoft Antimalware Service Executable are at the top of the list.

It's very frustrating, because this lasts anywhere form couple of minutes to up to 15 min and I can't do much at that time. If I kill the Microsoft Windows Search Indexer the system goes back to being responsive.

Is there anything I can do to fix this with exception of excluding Program Files from being indexed ?

You could disable indexing on the drive .. not solution but might give you some peace.

re-enable it after a few windows udpates have been added to your system

download your latest motherboard chipset driver from your Vendor.

Change your Sata drive cable, I have known faulty ones before that completely hang the computer. Doubt this is your problem though..