What are the relative advantages of various Python/PHP web frameworks (particularly for my project)?
Python vs PHP: Python
With python, you can always write wrappers for C code so you won't have to mess with starting other processes and passing args to them. That might be useful for your security functions. 
Web2py will allow you to easily write a webservice for this too, to more easily integrate the C portions with the web-site infrastructure. 
If you already prefer python, I would go with that. If you need to bring on web-developers later that are trained in PHP, teach them Python. It won't take long, and I'm sure they'll appreciate it in the long run. Plus, moving from a PHP MVC framework to web2py or even django would make things easier. I've used CodeIgniter for PHP and find that web2py was so much simpler and easy to understand. 
Also as for the directory structure, django is not actually true MVC -- it's MTV (model, template, view). 
I find web2py's organization a little more straight-forward. But yes, either way it can seem strange at first. I would say YES, you should bite the bullet and use MVC.
In web2py, the "view" is html markup with the ability to write raw python code. The controller extracts data from the model (database), attaches any needed files (css/js etc) and the model of course simply defines the structure of the data and allows you to access it in an OO way. 
Lastly, I wouldn't tip my hat in favor of web2py just because of jQuery integration. It does use it, and a some of the built-in framework stuff (like response.flash/session.flash, the LOAD function that loads a page or data from another controller) rely on jQuery, but using it in another framework only means you have to write an include statement (e.g. ). 
But, the way it allows/forces you to focus on development is what takes the cake for me.
I'm deciding on a web framework for an upcoming project, and I'd appreciate any advice. We've decided to use jQuery for the JavaScript, and are heavily leaning toward Python or PHP (more Python) for our server-side logic. I'm especially interested in web2py because of its jQuery integration.
About our project

Our project is to develop a security console for a complex
cybersecurity system operating within an organization's internal
network.
This console will be largely server-driven, as messages come in from the network and must be pushed by the server to the user.
The user will also be able to initiate security actions, the implementation for which will likely be in C++.
The interface we've planned will be relatively rich, and I want to leverage jQuery's power as much as possible.
We have some control over the browser environment we'll be running in (e.g., we don't have to worry about clients with JavaScript disabled).
Our site is likely to have only a few, long-lived client connections.
We are looking for software components with permissive licenses, though we're using some copyleft components (I see that web2py is LGPL while Django is BSD, so +1 to Django)
We have about a month to create a functional demo of our system, of which this interface is a small (but visible) part.

About us
We are two developers with about 5 years of programming experience, but little web development experience. I have several years of Python experience and a summers' worth of experience messing around with PHP. My coworker has some Python experience and has never touched PHP.
I used Django once back in 2008, and was frustrated by the file and code structure, which I found highly unintuitive. Perhaps this structure is inherent to the MVC model (I've had similar experiences with Django and CakePHP since), and I just need to bite the bullet and memorize it.
My Question
Given the information above, what are the relative advantages of the various Python/PHP web frameworks for our project? As mentioned above, I'm especially interested in web2py because of its jQuery integration, though Django's dominance is (once again) hard to ignore.
Thank you very much for your time!