EXM is built into the platform, so other than just disabling it via config, you don't have to do anything else to it.
You can ignore the following services and configurations if EXM has been disabled in the web.config:
The Dedicated Dispatch Server role does not need to be installed.
The EXM.Master database can be removed.
The EXM.Crypto and EXM.Authentication Keys in the ConnectionStrings.config can be removed.
Everything else should remain. However, I will respond to the other parts you listed.
The messaging database should be left intact. This database is used for the Rebus message queueing service that is part of the overall Sitecore Framework. While it's true that EXM is the first module to make use of it, future modules will most likely utilize it. I would leave this alone.
Marketing Automation is a sibling to EXM. It is part of the overall XP services that are offered for marketing campaign initiatives. The engine and reporting services you mention are part of xConnect. Not all of those initiatives utilize email. Leave it and the related xConnect services intact.