Caps,
I was able to get Subterfuge installed on Kali 2 (rolling-edition) with only a four commands.
My suspicion is that you are trying to do something more ;D
Here's what I did to get the install going.
In Brief:
root@localhost:~# git clone https://github.com/Subterfuge-Framework/Subterfuge.git
root@localhost:~# cd Subterfuge/
root@localhost:~/Subterfuge# python setup.py
root@localhost:~/Subterfuge# subterfuge
The Long Version:
root@localhost:~# git clone https://github.com/Subterfuge-Framework/Subterfuge.git
Cloning into 'Subterfuge'...
remote: Counting objects: 419, done.
remote: Compressing objects: 100% (25/25), done.
remote: Total 419 (delta 6), reused 0 (delta 0), pack-reused 392
Receiving objects: 100% (419/419), 4.43 MiB | 7.41 MiB/s, done.
Resolving deltas: 100% (149/149), done.
Checking connectivity... done.
root@localhost:~# cd Subterfuge/
root@localhost:~/Subterfuge# python setup.py
[+] Beginning Subterfuge installation...
Get:1 http://archive.linux.duke.edu/kalilinux/kali kali-rolling InRelease [24.6 kB]
Get:2 http://archive.linux.duke.edu/kalilinux/kali kali-rolling/main amd64 Packages [13.4 MB]
Get:3 http://archive.linux.duke.edu/kalilinux/kali kali-rolling/non-free amd64 Packages [145 kB]
Get:4 http://archive.linux.duke.edu/kalilinux/kali kali-rolling/contrib amd64 Packages [93.0 kB]
....
## Boring installation stuff here.
....
Installing collected packages: django
Successfully installed django
Cleaning up...
[+] Subterfuge installation completed successfully!
root@localhost:~/Subterfuge# subterfuge
Subterfuge courtesy of r00t0v3rr1d3 & 0sm0s1z
Performing system checks...
System check identified some issues:
WARNINGS:
?: (1_6.W001) Some project unittests may not execute as expected.
HINT: Django 1.6 introduced a new default test runner. It looks like this project was generated using Django 1.5 or earlier. You should ensure your tests are all running & behaving as expected. See https://docs.djangoproject.com/en/dev/releases/1.6/#new-test-runner for more information.
System check identified 1 issue (0 silenced).
You have unapplied migrations; your app may not work properly until they are applied.
Run 'python manage.py migrate' to apply them.
March 07, 2016 - 19:52:35
Django version 1.7, using settings 'subterfuge.settings'
Starting development server at http://127.0.0.1:80/
Quit the server with CONTROL-C.