You can't current delete an agreement completely, but they will never be shown to customers if you:
- In Settings -> Customers -> User Agreements
- Uncheck "Required For All" if you checked it off
- Uncheck "Required for Check Out" if you checked it off
- In Settings -> Inventory -> Edit Item Default Values
- If you made it required for checking out items of a particular item type, change the required agreement for the Item Type(s) to "No agreement required".
That will prevent the agreement from showing up to your users going forward while saving the full history of anyone who has signed those agreements (and what version they signed).