[mlir][python] Clear PyOperations instead of invalidating them. (#70044)

`PyOperations` are Python-level handles to `Operation *` instances. When
the latter are modified by C++, the former need to be invalidated.
#69746 implements such invalidation mechanism by setting all
`PyReferences` to `invalid`. However, that is not enough: they also need
to be removed from the `liveOperations` map since other parts of the
code (such as `PyOperation::createDetached`) assume that that map only
contains valid refs.

This is required to actually solve the issue in #69730.