You can archive historic Pay Spine Points by going to Admin > Personnel > Pay Spine Points
When you click Edit next to a particular spine point, you will see an Active field at the bottom. If you de-select Active, then click Update, the Pay Spine Point will be inactive.
It will be greyed out and fall to the bottom of the list of spine points as it is no longer in use. You will now not be able to be select this spine point on a staff contract.