Yes you can use a Custom Target list by adding only the representatives from a particular party.  Once you have the Custom Target list created and saved you can select during the Target creation of your alert.  If the constituent that is submitting the alert does not have a particular representative of this party in their state in would not allow the user to complete the alert.

Help documentation on creating a Target list: http://help.convio.net/site/PageServer?pagename=Admin_Advocacy_Managing_Target_Lists#to-create-target-list