I've been scouring the Blender Python API docs for 2.69x for a replacement to the 2.4x API's Mesh.getFromObject method.
I can't find any way to get a fresh copy of a mesh with modifiers applied in advance.
The option to apply modifiers is common for exporters included with Blender, so you can check how they do it.
Typically you can use the
It's important to remove the mesh, unless you have explicitly assigned it to an object. Otherwise it will be stored in Blender until the file is saved and loaded again.