A new version of the Salesforce Non-Profit Starter Pack Affiliation object has been released with the ability to turn off the automatic creation of Affiliations.
A new tab was added that enables control of the Affiliations so that they are not created automatically. When you upgrade your package, the behavior will not change, unless you turn it off.
Install link: http://foundation.force.com/packages/affiliations
Release Notes: http://wiki.developerforce.com/index.php/Nonprofit_Starter_Pack_Affiliations_Release_Notes