Fixing a couple cases that cause ProcessAllMessageQueues to hang.

The two situations are:
1. A thread is in the process of shutting down, so it won't handle any
   more messages.
2. A message queue is cleared before it has a chance to process pending
   messages.

In both of those cases, we should consider processing done at that
point.

R=honghaiz@webrtc.org, pthatcher@webrtc.org

Review URL: https://codereview.webrtc.org/2319303004 .

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Cr-Mirrored-Commit: fe7d091f57707efdb43f9c83470203369e59cfea