The packages from the ppa fix the issue for me. In order to reproduce,
install neutron-vpn-agent from Newton UCA and run:

# mkdir /tmp/test
# ip netns add testns
# ip netns exec testns neutron-vpn-netns-wrapper --mount_paths 
"/var/run:/tmp/test" --cmd "ipsec,status"
2017-02-07 18:17:06.729 17492 INFO neutron.common.config [-] Logging enabled!
2017-02-07 18:17:06.730 17492 INFO neutron.common.config [-] 
/usr/bin/neutron-vpn-netns-wrapper version 9.0.0
Command: ['ipsec', 'status'] Exit code: 0 Stdout:  Stderr: connecting to 
'unix:///var/run/charon.ctl' failed: Permission denied
failed to connect to stroke socket 'unix:///var/run/charon.ctl'

With fixed package:
# ip netns exec testns neutron-vpn-netns-wrapper --mount_paths 
"/var/run:/tmp/test" --cmd "ipsec,status"
2017-02-07 18:21:29.119 22248 INFO neutron.common.config [-] Logging enabled!
2017-02-07 18:21:29.120 22248 INFO neutron.common.config [-] 
/usr/bin/neutron-vpn-netns-wrapper version 9.0.0
Command: ['mount', '--bind', '/tmp/test', '/var/run'] Exit code: 0 Stdout:  
Stderr: 2017-02-07 18:21:29.126 22248 INFO 
neutron_vpnaas.services.vpn.common.netns_wrapper [-] /tmp/test has been 
bind-mounted in /var/run
Command: ['ipsec', 'status'] Exit code: 3 Stdout:  Stderr:

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https://bugs.launchpad.net/bugs/1587886

Title:
  strongswan ipsec status issue with apparmor

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