It's a trivial change: first, Delete the Unit. Then, use the deletemissingreferences command to remove any other entry in any table that references UNIT_MECH. There, two lines and you're done.
As for this:
Seems like I am the only one considering GDR imbalanced and alien
It's SUPPOSED to be imbalanced. That's the whole point. The entire Modern Era was deliberately set up as an endgame, with a massive increase in raw power that quickly makes any previous eras' content obsolete, and that extends to the few things in the Future Era as well. It's not supposed to be a stable, balanced environment; it's designed to get the game over with, breaking any stalemates.
The GDR is supposed to be a "wait, you haven't won YET? Okay, here's the Easy Button. End it already." sort of unit, but it's hardly the first. The jump in power from Tanks to Modern Armor, from Bombers to Stealth Bombers, from anti-tank guns to Gunships, etc. are nearly all larger than the jumps between previous generations of units, in far less time. If I have Modern Armor and Stealth Bombers and you only have Tanks and Bombers, I'm going to wipe the floor with you militarily, despite the fact that these are separated by only a handful of techs.
Similarly, the Research Lab, Broadcast Tower, Stadium, and Medical Lab are basically designed to make it so that the civ that reaches these eras first pulls ahead and can finish quickly. They're not even close to balanced (although the revision to the Broadcast Tower in this last patch makes it a LITTLE better). You also see this on some of the Wonders, like the post-patch Eiffel Tower and Sydney Opera House.
I had to deal with this extensively in my own mod, which adds lots of future content; you can't have this sort of endgame imbalance now falling in the middle of your tech tree, so I had to heavily modify a lot of the content of that era. Obviously I removed the GDR, but I also had to adjust nearly everything in the Modern Era for balance reasons.
