You only need to disable the resident feature of Spybot-S&D. And that is the way to deactivate it: Run Spybot-S&D, switch to the Advanced mode via the menu bar item Mode → hit Yes → select Tools in the navigation bar on the left → Resident and there you can untick the checkboxes in front of the two tools.
But warning! Then you will not have resident protection!
If you are using Spybot 2, please see here for instructions to disable Live Protection.