Just tried it (on Ubuntu, apache 2.2.20), and it worked fine for me, even without fiddling with the default_* / master_* options. I.e., the ssh master connection etc. is automatically being terminated properly.
Maybe enabling debugging
$Net::OpenSSH::debug |= 0x7f;
will shed some light on what isn't working in your case (output ends up in the webserver's error log).
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