I guess it depends a little on what you mean by integrate. I know of a customer that has an application on Dynamics and uses Ensemble to integrate with some back end systems. Dynamics itself is very much tied it's data model. If you want to call out to another system for data to use in Dynamics, I think you'll want to look into best practices from Microsoft. But as a messaging platform, Ensemble should support most integration needs well. If you have a specific protocol or standard in mind you might verify that it is available in the adapters that ship with Ensemble.
I'm not at all familiar with this eCQM package, but I don't see any reason it wouldn't work on IRIS. Just import the code. The system interaction and device handling is where you would be most likely to encounter issues. The VistA Kernel encapsulates these and so insulates application code from those details. You may not encounter issues with Kernel but if you do, solving them would require an advanced level of VistA skills. I think the easiest/fastest path would be to just load it up and see what breaks. It may be that you can get your work done without any issues.
There are several alternatives described in the standard. Check out section 4.3 and section 5 at this link http://docs.oasis-open.org/security/saml/Post2.0/sstc-saml-tech-overview-2.0.html
I have seen an implementation of SSO where the information that would be in a SAML token is passed in http headers. This implementation used delegated authentication to sign in the user based on these http headers. This link is to documentation for delegated authentication https://docs.intersystems.com/latest/csp/docbook/DocBook.UI.Page.cls?KEY=GCAS_delegated
You might also consider using OAuth if you are using a REST interface. https://docs.intersystems.com/latest/csp/docbook/DocBook.UI.Page.cls?KEY=GOAUTH
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