Simple Matrix Rotation
Unnecessary matrix generation

In JavaScript, Arrays don't have a fixed size. For example, you could do this:

var arr = [];
arr[324] = 91;


with no problem.

Your GenerateMatrix function is really over-doing it. All you need to do is create the arrays for the rows/columns then change their values.

And, you can do that with a neat trick:

Array.apply(null, Array(rowCount)).map(function(){return []});