Discussed this with GvR.
Here's a recap:

For 2.6 and 3.1 which are already released, check for the _fields attribute.  This is a guaranteed part of the API is not fragile.  For the C structures, check for the n_fields attribute.

In the future, the C API needs to grow to match the namedtuple() API and we should add an abstract base class describing the common API.  Then you'll be able to write: 
    if isinstance(obj, abc_namedtuple).