I'm afraid you're very right on this...
I think CA (or Sega, I don't know) would be ok with people modding their games, as long as it wasn't that people try to transform the game into a completely different game in a different era.
If modding tools would have been released for ETW, then surely there would have been modteams jumping on the oportunity to convert ETW to the classical era. Of course CA wouldn't risk that to let their sales of a possible R2TW drop.
Now I think most people would buy R2TW anyway (eg, besides the existing mods for RTW that converted it to the medieval era, M2TW was still a success), but it's still a risk and companies don't like risks...