As people will probably tell you, they're two different lenses and it really depends on what you plan to do with it.
The canon would be better for general hand held macros, due to the IS, and has a 1:1 reproduction ratio, so think about if you really need that, plus it's also weather sealed.
Though on the otherhand, a completely different beast, I find 1:2 is enough for me, the zeiss is stupendously sharp, at f2 it's sharper than the canon at f2.8, though with macros you'll probably be stopping down anyway, but the micro contrast is amazing, which is what people refer to as the "zeiss look", and it doubles up as an amazing portrait lens, 100mm is my favourite FL for portraits and f2 with creamy zeiss bokeh, amazing micro contrast and super sharp is a great recipe for 3d isolation portraits. Here's a comparison of 1:1 (simulated) and 1:2,http://www.the-digital-picture.com/Reviews/Zeiss-100mm-f-2-ZE-Makro-Planar-Lens-Review.aspx
I'm not too fussed about MF as well, you can live view for macros or just use the focus confirmation, it works well for me. The zeiss isn't weather sealed but it's built like a tank, if I were you and had money to burn I'd go for the zeiss for its uniqueness, but if you need IS and 1:1 then the canon is also a mighty fine lens and won't disappoint!