Closure Compiler doesn't rename anything using string syntax (Object["property"]). Everything using dot syntax (Object.property) is renamed.
So if you add a function to the window object using string syntax:
window["MyFunction"] = function () {...};
you should be able to call it from C# using the same syntax, and it will survive minification, e.g. by executing the string:
"window[\"MyFunction\"]();"
Usually for robustness I add a check that the function exists, to prevent it crashing in case it tries to execute that before your plugin has created the function:
"if (window[\"MyFunction\"]) window[\"MyFunction\"]();"
In short, if anything is sensitive to being renamed, use string syntax.