That doesn't sound like much of a choice. $500 for a worse lens that perhaps is slightly more magnified?
From what I have read - just read - it does seem like the 180mm macro could be sharper, and could perhaps be faster (although most lenses can't be made arbitrarily fast...the new EF extenders make lenses focus much slower for the sake of accuracy, especially the 2X).
I know - I'm not employed by Sigma - but I do recall that they have a pretty new (I think, there's also a discontinued one I might be getting this mixed up with) 150mm macro which should be more or less close to the 180mm macro, but at the usual bargain basement prices.
Edit: Nevermind - I looked down that road before - TDP finds problems with AF accuracy with Sigma's semi-equivalent offerings to Canon's 100mm f/2.8 and the 180mm f/3.5 macros - the 105mm and 150mm macros, both f/2.8. Both are reported as having AF issues "even on 1-series bodies." Vignetting on the 150mm. Sharpness for both lenses wide open is about the same as their Canon equivalents, even on the f/2.8 150mm compared to the 180mm - not bad.
Personally I haven't heard of any replacement for the MP-E 65mm...being able to focus and change the variable magnification at the same time is something no other lens, at least on EOS, does so smoothly. No excuse not to get it if you need it. It really has been a boon for miniature photography, and much better than some clumsy reversed-prime (exposing the wrong end of the lens to the elements, for goodness sake!) ordeal which still doesn't let you easily change magnification (well, depending on how bad the bellows is I suppose). If I recall right you can eat the cost of a MP-E and the macro twin light and still have a few dollars left over before you can buy the 180mm macro, which of course won't be coming with a macro light. On the other hand, the detachable flash heads on the twin light should be very useful for the 180mm macro too.
For my first dedicated macro, I'll probably be looking at the 100mm f/2.8, although the 180mm f/3.5 is still tempting - but being half again more expensive it doesn't seem quite to add up the value I expect. No extender utility with the 100mm, though IS more than makes up for it I would expect. On the other hand...180mm!! Of course, if money were no object, the Hartblei Superrotator 120mm f/4 Makro would be a tempting choice too.