I am curious how things have progressed with your Input Method submission to the Mac App Store? If nothing else, could you share the details of Apple's rejection of your submission, e.g. did it specify the section of the Mac App Store Guidelines that were violated by your app?
In reading through the Mac App Store Review Guidelines, it seems like 2.14 and/or 2.15 would be the relevant obstacles for App Store distribution of an Input Method component:
2.14 Apps must be packaged and submitted using Apple's packaging technologies included in Xcode - no third party installers allowed
2.15 Apps must be self-contained, single application installation bundles, and cannot install code or resources in shared locations
since Input Method components need to be copied into ~/Library/Input Methods or /Library/Input Methods.
I'm in the early stages of my own Input-Method-based project, and it would be helpful to know for certain that Apple App Store distribution of such a project is not allowed (at which point, Apple's Distributing Apps Outside the Mac App Store looks like the official starting-point, and a post like Releasing Outside the App Store seems like a good read).