Yeah i was having similar battle problems at times but I have found that waiting does really work for most of it. Also, I partially blame the SLI mode I'm running in, but at least the board keeps some space between the cards. From what I can tell my cards stay relatively cool which I know reduces my CTDs, especially compared to my old computer. There is of course the good old RTW memory leak issue which is a constant of the game. Given enough time it'll even begin to eat through the 6 GB of RAM I have (we're talking the greater portion of a day but it will happen), at which point a CTD is inevitable.
If loading times aren't too bad (under a couple minutes, preferably under a minute), I'd recommend the wait after battles + take a break every 3-4 hours to minimize the risk of CTDs.