The following code is borrowed and slightly modified from "Non-blocking read on a subprocess.PIPE in python"  (kudos to J.F. Sebastian - if you accept this answer, please upvote the original code)
import sys
import time
from subprocess import PIPE, Popen
from threading  import Thread
try:
    from Queue import Queue, Empty
except ImportError:
    from queue import Queue, Empty  # python 3.x
ON_POSIX = 'posix' in sys.builtin_module_names
def enqueue_output(out, queue):
    for line in iter(out.readline, b''):
        timestamp = time.time( )
        queue.put((timestamp, line))
    out.close()
#-- This is how long you're willing to wait before you 
#-- consider your Spynner process to be brain-dead.
MAX_WAIT_TIME = 300.0  #-- we'll wait 5 minutes (300 seconds)
#-- Construct a shared queue that will be used to send messages from 
#-- the subprocess I/O polling thread to the watchdog (main) thread.
q = Queue()
#-- Spawn your subprocess...
p = Popen(['myprogram.exe'], stdout=PIPE, bufsize=1, close_fds=ON_POSIX)
#-- Create a new thread that runs in the same process as the watchdog.
#-- This thread will poll the output of the subprocess and populate the 
#-- shared queue.
t = Thread(target=enqueue_output, args=(p.stdout, q))
t.daemon = True # thread dies with the program
t.start()
#-- Now, we'll try to read from the shared queue.
try:
    #-- Queries the shared queue for the next item in the queue,
    #-- waiting for up to MAX_WAIT_TIME before failing with an Empty exception.
    timestamp, line = q.get(True, MAX_WAIT_TIME)
except Empty:
    #-- Ok...the queue is empty and it's been MAX_WAIT_TIME since
    #-- We've pulled anything from the queue.
    p.terminate( )  #-- "terminate with extreme prejudice"
else: # got line
    #-- Got a (timestamp, line_of_text) pair, where the timestamp is the
    #-- system time when the I/O polling thread grabbed the line from
    #-- the subprocess pipe.  This timestamp isn't strictly necessary,
    #-- but might come in handy in debugging the brain-dead Spynner process.
    #-- So now...do something with that line of text!
    doSomething(line)
You'll have to augment this code with some logic for spawning a new Spynner process to pick up where the terminated one left off, etc., but hopefully this should give you an idea of how to proceed.