There is a question already on StackOverflow on how to do this in C#. I'm afraid I don't know what you need to do to directly call these APIs in Python, but I imagine it is very similar, especially if you're working in IronPython.
Edit: Unfortunately, further reading on StackOverflow also heavily cautions away from using this API. Quoting the MSDN documentation on SuspendThread:
This function is primarily designed
for use by debuggers. It is not
intended to be used for thread
synchronization. Calling SuspendThread
on a thread that owns a
synchronization object, such as a
mutex or critical section, can lead to
a deadlock if the calling thread tries
to obtain a synchronization object
owned by a suspended thread. To avoid
this situation, a thread within an
application that is not a debugger
should signal the other thread to
suspend itself. The target thread must
be designed to watch for this signal
and respond appropriately.
It seems the preferred method is some form of cooperative multi-tasking, but my searches for this sort of feature in ffmpeg have not resulted in any promising results. SuspendThread() may be your best option at present, unless you add hooks into ffmpeg itself to support suspend requests.