There are lot of folks who run Crossfire and SLI who would tell you that its not a problem at all. This is talked about quite a bit here on the forums, just do a search and you'll find some threads. There was one recently where a guy had linked a video on Youtube that showed the effects of the so called, "micro stuttering", funny thing was, he had to record the monitor with a high speed camera, and slow it way down to like 2 frames per second to actually see it and demonstrate what it was! Hello, if I have to slow it down that much, I ain't going to be playing it anyway. I think this is more of an item hardware and benchmarking sites have locked onto because they are having problems finding anything else interesting to report on, and when you find a potential hardware "problem" it grabs everyone's attention, honestly. I have ran both Crossfire and SLI, currently running 2 560ti's in SLI, and it looks nothing to me but smooth and fast. I think I do prefer SLI, just seems to me that the scaling is a little better over a wider variety of games.
Jit, I think its like 60hz CRT monitors. I still have two of them here in the house. Those that use them think they are fine. My mother and father both don't mind CRTs. But when I sit at the computer they don't understand why the FIRST thing I do is up the refresh rate to 72 or 75hz. I sit and use a 60hz CRT and my eyes INSTANTLY hurt. I can it. My mother, father, roommate, and best friend all have no idea what I'm talking about. I think MS is like this. Not everyone can see/feel it, but those who can can't stand it. For the record I've never used a CF/SLI machine so I have no idea if it would bother me or not.