Though I'm a Nikon shooter, I have some suggestions:
I've seen macro with excellent results with both - as you can expect, both are well capable of stunning results.
The 5D2 is full-frame, and the Mk4 is 1.4x (I think), so you get more magnification with the Mk4. However, depending on your subject, you're likely to get more detail with the 5D2, and the full-frame sensor means you have a bit more scope with depth-of-field effects.
Since autofocus is generally redundant for macro, there's no advantage having the Mk4 over the 5D2 for AF performance if the sole use is macro work.
Noise isn't usually a concern with macro users, since the majority use very low ISOs and relatively long shutter speeds on solid (ie expensive!) tripods/heads (esp. if using lenses in the range of 100-200mm, or else Canon's amazing MP-E65). However, using a rather different handheld flash technique (using a diffused flash very close to your subject at full power, and deliberately underexposing the shot by about 1 full stop) you can get very versatile handheld compositions utilizing the high ISO potential of the Mk4 (similar I guess to what I do with my D3S which I use with a 200mm, with shutter speeds as fast as 1/250-1/320 at f16 all the way up).
Other considerations which might have an effect here: the full-frame 5D2 is also an excellent tool for landscape photography (where its low frame rate doesn't hurt and its high resolution wins out). The Mk4 is an exceptional birding camera. If you wanted to get birds as well, the Mk4 would be the better option, esp. considering that using it with a 300mm f4 lens would also produce an excellent dual-purpose bif and dragonflies/butterflies pseudo-macro setup.
Other than that, the price difference reflects pro-quality features and build on the mk4, but would you be paying for features you'd never find useful?
