OK, I updated the obfsproxy apparmor profile so it works for both standalone and managed obfs3. Needed to add a line to /etc/apparmor.d/local/system_tor too. Profiles below and included in the attachment along with an init.d definition.
/etc/apparmor.d/usr.bin.obfsproxy
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#include <tunables/global>
# vim:syntax=apparmor
/usr/bin/obfsproxy {
#include <abstractions/base>
#include <abstractions/python>
network inet stream,
/dev/random r,
/dev/urandom r,
/etc/nsswitch.conf r,
/etc/passwd r,
/usr/** r,
/usr/bin/obfsproxy rix,
/var/log/tor/obfsproxy rw,
signal (receive) set=("term") peer=system_tor,
}
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/etc/apparmor.d/local/system_tor
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# Site-specific additions and overrides for system_tor.
# For more details, please see /etc/apparmor.d/local/README.
signal (send) set=("term") peer=/usr/bin/obfsproxy,
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