I realize I'm a few months late but there are actually several ways to control a mesh deforming armature from within BGE without rewriting the source code. Here's probably the simplest method:
- Create an anchor object such as a cube. The size, shape, and location are unimportant.
- In pose mode, select the armature you want to use and add the bone constraint "copy rotation", then choose your anchor for the target.
The rest should be pretty self explanatory. As you rotate the anchor (using python or logic bricks) the armature mimics it and deforms the vertex group it's assigned to. If you're using this with something complex, like a humanoid model, then you'll probably want to use a script. If you're uncertain how to do this a good example is the "brik" ragdoll plugin"brik" ragdoll plugin. The source for brik will show you how to easily search for bones in any armature and automatically create, name and assign anchors in just a few lines of code.