The gory details of the current startup situation are in PEP 432. However, the comprehensive solution described in that PEP isn't going to make it into Python 3.4, so a simpler interim fix would be worthwhile.

Since Blender is designed to support building against the system Python, the trick of forcing Python to link to an alternate implementation of a function won't work.

Inspired by http://docs.python.org/3/c-api/init.html#Py_SetPath, I suggest offering an API like:

int Py_SetStandardStreamEncoding(char *encoding, char *errors)
{
    if (Py_IsInitialized()) {
        return -1;
    }
    Py_StandardStreamEncoding = _PyMem_Strdup(encoding);
    Py_StandardStreamErrors = _PyMem_Strdup(errors);
}

The initstdio function in pythonrun.c would then be updated to use the specified Py_StandardStreamEncoding and Py_StandardStreamErrors if they weren't NULL (since that would indicate an embedding application had called SetStandardStreamEncoding).