Address reference leak issue (fixes #1029)

Creating an instance of of a pybind11-bound type caused a reference leak in the
associated Python type object, which could prevent these from being collected
upon interpreter shutdown. This commit fixes that issue for all types that are
defined in a scope (e.g. a module). Unscoped anonymous types (e.g. custom
iterator types) always retain a positive reference count to prevent their
collection.