Hey there jabberjaws! That is a great question, I respect where you are coming from, so I'd like to give you a thorough and complete answer.
Currently GRM = latest version of Crusade and will have a separate mod folder for GRM Intrigue content. The "intrigue patch" will eventually go away (later this month or next).
Unless Stardock drastically changes something about Intrigue files, all you will have to do in the future is remove the "GRM-Ideology for Intrigue" and "GRM-Governance" folders from the Mod folder. Don't look for them yet, they will be in the next version of GRM.
From now on I'll leave up older versions of GRM for the last non-beta version of Crusade, as I hadn't thought about GOG people not having access to Beta versions... and I don't begrudge them.
What will NOT be supported with consistency or at all (I promise you nothing but the ashes of your tears and the blood of your most beloved hamsters and other supported pets)
Galactic Civilizations III without Crusade and Mercenaries
This will CHANGE if new expansions are similar to Crusade (which change the whole base-game).
Why won't I support Galactic Civilizations III without the "expansions" or a particular DLC if I choose to?
1) Because it would create a great deal of extra work.
2) Because it would create a more difficult and annoying installation process for users, I know it shouldn't be hard, but I'd be dealing with a lot of people messing up versions and installations. I HATE bugs. I quit a game I was 4 hours deep into and abandoned it this weekend, because I found a TYPO in the Fulgar's custom speech (its fixed... they are "interested" in new things... not "interesting"). So many people will 'think' they found a bug because they installed the wrong version. I will end up wasting many hours chasing illusions.
3) Because I support StarDock, and they, by creating more content and updating their games, support me. I choose to only support their latest versions. If a DLC is packaged in a way where I can make a separate mod folder and make things modular for you... sure, great! If not? Than unfortunately I choose to push forward and I won't be ensuring backwards compatibility.
So jabberjaws... I think you'll be OK, you've got Crusade, and I think its unlikely we will see a expansion that replaces the base game again... so its unlikely I'll have to support a non-Crusade version, and everything will be modular. For those who don't have Crusade... the afore mentioned ashes and blood is all you get from me 
Thanks for reading, if you need a particular old GRM version right now, I know you're a long time and appreciative fan, PM me and I'll hook you up.