Microsoft CRM Connector for Microsoft Dynamics GP Setup does not allow installation to proceed if BizTalk Server 2004 is already installed. However there is a registry setting which can be used to turn off this check.

Registry key name: HKLM\Software\Microsoft\MSCRMIntegration

Set the string value of UseExistingBTS under above key to 1 to avoid installation and configuration of BTS 2004 by Integration.