In case anyone else finds this thread with the same errors I was having trying 
to get 2 factor authentication to work, using OpenConnect with vpnc-script 
worked for me. 
apt-get install openconnect then
openconnect --script /etc/vpnc/vpnc-script https://vpn.example.com/
http://www.infradead.org/openconnect/vpnc-script.html

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https://bugs.launchpad.net/bugs/1371817

Title:
  vpnc doesn't handle 2-factor authentication, but a fix exists

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