Fortunately for us, this setting is made in the registry. That means we can script it in any instance where we need to deploy this setting change through our enterprise environment.
reg add "HKCUSoftwareAdobeAdobe Acrobat9.0JSPrefs" /v bEnableJS /t REG_DWORD /d 0 /f
Adobe Reader 9.0
The value in the registry can be found at a similar path:
reg add "HKCUSoftwareAdobeAcrobat Reader9.0JSPrefs" /v bEnableJS /t REG_DWORD /d 0 /f