libmikmod installs fine for me on Mountain Lion.
ld: in /opt/local/lib/libxml2.2.dylib, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 6 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): /opt/local/lib/libxml2.2.dylib for architecture i386
That's a pretty strange message. I found a few occurrences of it via Google but didn't see a conclusive solution. But it makes me think that some part of your developer tools, possibly ld, is out of date. Please ensure that you have installed Xcode 4.4.1 via the Mac App Store, and opened Xcode and gone to its Preferences window, to the Downloads tab, and installed the latest Command Line Tools from there.