I'm afraid that there is no single pronunciation- it could vary depending on the meaniong and the emphasis. In your first sentence, there could be stress on any of the words depending on the meaning:
THEY were alone. (not someone else)
They WERE alone. (at that time)
They were ALONE. (no one was with them)
And this would affect the pronunciation. However, in general speech, unless I wished to emphasise one of those point, I'd use /wərə’ləun/.
Student or Learner