Like I said, for the most part I do try to keep my rep clean. I've had quite a few spotless games. However, I will sometimes do a "pre-emptive" strike if a nation (particularly a fundy one) keeps violating my territory. For some reason I'm not as squeamish about backstabbing those annoying fundies--I don't like fundamentalists in real life either!--but I make sure I CAN strike quick, sure, and with extreme devastation because if not, they WILL recover quickly! But I generally only strike pre-emptively if they keep violating their side of the treaty--i.e. putting units in my territory and I've warned them a few times, etc. IMHO, that SHOULDN'T hurt your rep (they keep violating the treaty), but somehow it still does. I just get pissed off and do it--and if I have the UN, I sometimes send the delegate over after I've done max damage (try to in one turn), and if they talk at all, they must offer a cease-fire (I did this once AFTER taking an enemy city that had the UN once, BTW...it was funny)! Also with the SoL, I can go back to republic again the same turn (assuming I had to switch in the first place), or democracy (lately I've been trying my hand with that, and when you're BIG with certain wonders it actually doesn't work out as badly as I thought it would!).
I did an experiment once--an enemy civ had kept putting units back in my territory after two or three warnings. This time he had some offensive ones (tanks) thrown in there too. The previous warnings, he gave the usual apology and moved out, only to keep moving back in the next turn. But this time it looked a bit different, so I saved the game, then sent my emissary to do the usual b*tching, seeing if I could head off a sneak attack (I had the UN). Well, this time he was tired of my "vile provocations" or whatever they say in that situation, "Prepare for war!" (which I didn't think they could do if you had the UN). I then restarted the game, and didn't say anything this time. Sure enough, they sneak attacked that turn! So I restarted again and did the original routine, and had myself a nice enjoyable rout of their forces (since they made the remarkable mistake of starting a war with me when it was MY turn!).
Took a city, they asked for peace, and never even got a shot off!
Yes I know, btw, if you are commie (or fundy, etc.) you can demand tribute and that MAY start a war.... But sometimes even then the civ will avoid the issue ("we ignore your feeble threats")--usually when relatively weak but still a nuisance....