Unfortunately checking the numbers against eachother probably isn't going to tell you much.
You can do things like run a Smart List with a date constraint and a specific page and see how many of each sort of visitor you got, but because they are different scripts and things are counted differently the numbers basically never match exactly.
When you say better workaround, what's the business goal? GA has some great aggregate metrics, while Munchkin is more single-lead based. With some lists you can get to things that are similar, but usually I use both tools but answer different questi with each.