Sure. But because I see this as sort of a fringe case and because I don't want to muddy the workflow with a user-visible settings interface, the setup is going to be a little complex. You'll have to run a search once to create the file ~/Library/Application Support/Alfred 2/Workflow Data/com.danielsh.alfred.its/settings.json. That file should contain an empty JSON object. You just need to add the key--value pair "affiliate_string": "&partnerID=2003&tduid=NL1380330" and your affiliate information will be added to the links that the workflow generates. Other users can of course do this as well, with their own affiliate strings.
