The HPT cannot be completely disabled, but if you just don't use it, that is enough.
I _strongly_ advise against using the HPT controller. I was fortunate in that I noticed how awful it was before it did any permanent damage.
How can I stress this enough?
Don't use the HPT3666 controller! It's a POS! It will cause data loss and eventual hard disk failure!
Either use the standard IDE1 and IDE 2 ports, or do what I did and get a fast Promise PCI IDE controller card.