If you simply want to be able to minify a javascript string in C# before saving it to a file, I would use either the MS Ajax Minifier or the YUI compressor for .net. Both of these expose an API that allows you to do this. Here is a sample using the ajax minifier:
var minifier = new Microsoft.Ajax.Utilities.Minifier();
var minifiedString = minifier.MinifyJavaScript(unMinifiedString);
Using the YUI Compressor for .net:
var minifiedString = JavaScriptCompressor.Compress(unMinifiedString);
Both the ajax minifier and and YUI Compressor libraries are available via Nuget.