I'm sorry, it might be only me but I really don't understand your question.. What are you looking for? Is Microsoft CRM a web app and you want your users to to have SSO access while you have a simple management and tracking? Then Horizon is your product. If Microsoft CRM is a Windows app you could package it using ThinApp and manage and deploy it to your users using Horizon or using any existing tool you may have..
ThinApp is a packaging format. It provides easier deployment, management and support of Windows based applications.
Horizon is a desktop aggregator. Your users should have one single place to access all their work related stuff while the administrators have much more control and a easier to maintain system.