Remove use of thread for greedy_pauli_optimisation

[sjdilkes]

Threading seems to be causing incorrect circuits to be produced that testing missed. Given we aren't multithreading, we can get the same performance by just doing manual checking on the timeout, which this PR adds.

Checklist

• I have performed a self-review of my code.
• I have commented hard-to-understand parts of my code.
• I have made corresponding changes to the public API documentation.
• I have added tests that prove my fix is effective or that my feature works.
• I have updated the changelog with any user-facing changes.