The .map file is used for debugging (for example, there are new features in Chrome that let you 'map' into the non-minified version of the source).
If you're using bundling/minification you can link to the full version of the file, so you can delete (or move) the .map file safely and the code will work again, and you'll still get minification through the MVC framework.
As a note, I'm assuming you're not doing any jQuery library work here, and that you're not currently needing to access the non-minified version while debugging in the browser. More often than not, I'm a "consumer" of jQuery and tend not to look into the black box.
For more info, Elijah has some great info on the point of the source map and how you can use it.
http://www.elijahmanor.com/2013/01/the-magic-of-jquery-source-map.html
As well, if you want to implement a temporary workaround to address the map minification problem (may be related) you can check out this SO question: jquery 1.9.0 and modernizr cannot be minified with the ASP.NET Web Optimization Framework