It may be easier the include both logo on different layers in your template psd file run your data driven graphics job. Then process the populated output files with a script that would retrieve the department and delete the logo layer that does not match the department. Or leave the template as is have the script just retrieve the department and add the correct logo to the populated output files.
With data driven graphics and datasets you have several choices. You could have several logo layers and use the data to control which is visible. I think that would be the best way. You could use the dataset to replace the contents of the logo layer. That works best if the logos are the same size. Either of those could be done with simple changes to the template and datasets. You could post-process the images as suggested if you can't change the datasets.
Thank you for the help. I think indeed the easiest way is to get all the logo into the data set source.
The file I'm getting does not includes the logo but I can easily write a program that will update it and add the missing things.
Thank you again.