Apparently I totally missed the big discussion, but let me add my two cents:
First, the "solution" of just garrisoning and resting your troops outside the city is somewhat less attractive if you have Sun Tzu and thus a free barracks IN the city (this is particularly true when resting armies and Elite units). I was somewhat perplexed by the culture flip myself recently. Playing as the Americans on a Large map, decided to attack the Japanese to my north to grab the sole oil reserve on the continent. Realized holding that city could be a problem, and also realized I had a lot of extra troops and their capital only one city away from mine (for some reason, we were fairly close in the beginning of the game - this is also deceptive because our borders are about four or five each. So my second attack is on their capital. I also capture two other cities on my border, and push their capital back. Needless to say I was very frustrated when my entire army (two armies, and a dozen units) was lost on a double flip of Kyoto and Tokyo. The flip was perplexing - MY capital wasn't all that far, and the next ring of cities were Seattle and Philadelphia, both huge massive culture producing cities with at least a wonder or two in them. And as I said, I had a few troops. I guess I now understand why it happened.
Incidentally, I didn't just accept it - I went back to see "what went wrong." Sure enough, both cities had unhappy citizens (more happy than unhappy, but unhappy ones, too). When I got rid of the unhappy ones and continued again, it didn't flip. I'm pretty sure watching attitudes keeps things kosher, although I might have just changed the random number.
At any rate, I've learned my lesson. From now on I will just bombard the cities and get their pops down. A strategy I will put to great effect when I take the French's two oil reserves in my next way.
I do think that your troops should "retreat" and relocate to either the edge of the city, your nearest city, or the capital. That would be logical and "accurate."