I also keep trying to think of a way to make ThaneMOD work with CEM but...I'm not sure how to do it. I mean, I suppose someone could swap in the Thane model for Kolyat and rework the entire memorial scene but with the limited dialogue options from Thane in ME2 and 3, is this even possible to pull off? Or maybe just figure out a way to have him in the goodbye scene? I can't offer much other than some audio and maybe a little dialogue work but if people think that's a good idea I wouldn't mind looking into it.
Keeping in mind that I don't have Citadel DLC, so I haven't played it or your mod, as far as I know, it allows you to play the Citadel DLC content after the end of the game. Correct? The whole mission, plus all the apartment and party content, yes?
There should be no complication with the Memorial Scene, Deager. I'm guessing you haven't gotten around to that ThaneMOD PT yet 
From our previous PMs over on ME3Exp, my impression was that you hadn't changed any conditionals involving Thane for CEM. If that's the case, everything should work fine, since the Memorial Scene won't trigger. It doesn't with unmodded Citadel DLC, so unless you changed a conditional, then it won't trigger with CEM. That also means that Kolyat is absent for the entirety of the DLC.
Putting Thane back for CEM is something that I would need to discuss in detail with folks on the ThaneMOD forums. It's a big decision. Even after the ending it's complicated because of the new lore established in the emails. Here's why:
Friend-Thane has a different fate than LI-Thane. Friend Thane is nowhere near the Citadel even at the end of the game. He's receiving treatment for his illness on Kahje, getting ready to head to Noveria. His health has improved, but he's certainly not combat ready, and could still die (we allow enough room for players to headcanon as they wish). While he expresses his desire to rejoin Shepard (to help fight the Reapers) in his final email, I'm not sure he would feel the need to rejoin Shepard for a party. We also really don't have dialogue appropriate for him for that situation, and I'm not a fan of implementing things into a mod that feel "forced."
LI Thane is different. He "joins" Shepard aboard the Normandy sometime after Horizon. And, one of the things on the list for v2.0 is to actually place him there and give him a romance scene. This, of course, may or may not be possible. We haven't started looking into it hardcore yet; we've just started talking about it. However, because of this, I wouldn't want you dipping into any of Thane's dialogue for CEM. If we can create this scene for v2.0 (likely working off of Garrus or Sam's scene or something; parts of Kaidan's would be really nice), we're going to need as much dialogue as we can get our hands on. And, because I've already used Thane's best dialogue for Huerta, I might even need to re-tweak that.
So, I guess for now, I appreciate the offer, but it's not the right time to pursue it. It may or may not be something we can look into (if you are still willing) once development is further along on TMv2.0. Should know more in a couple months...I hope.