You might also want to take a look at https://github.com/madscientist/msjnc. I found it a lot better than Juniper's manager for linux.
> A number of people have written me to ask about multi-key logins. I don't have any knowledge of or experience with these and my (very limited) investigation of the Network Connect service doesn't show how to do this from the command line. If someone can describe what the expected interface to the ncsvc program is for these situations I'll try to add support for it.
http://mad-scientist.us/juniper.html
At least that sounds like two-factor authentication he's talking about ("multi-key logins"). If it supported that I would definitely use it.