I have gotten this to work recently without intervention. 

Firstly, download the python source code for the library you want to upload (i.e. don't pip install it). 

On a linux machine (I used ubuntu-14.04.3-desktop-amd64 on a virtual machine), compile the library by navigating the library root folder and

 sudo python setup.py install

It will display the site-packages folder that it creates the library files in. 

What you will need to do after this is upload the entire library folder (for example pandas) to the Resources>Engine>Plugins>Python>Python27 folder on FME Cloud. Navigate to that folder, highlight Python27, then click "upload" in the top left of the resources container. Once there upload the folder. Now you can call it as you would normally in your python script using

import

 sudo python setup.py install

import

Thanks for posting, this functionality has indeed been much improved since my original reply.

Here are some instructions I wrote up previously.

https://pypi.python.org/pypi/PyExecJS

Instructions

FME Desktop:

• Open command prompt
• cd to directory with where setup.py is located
  
  • Windows: fme.exe python easy_install PyExecJs
  • Linux: fme python easy_install PyExecJs

https://www.dropbox.com/s/zi09xcgus1ysten/Screenshot%202015-08-28%2017.24.49.png?dl=0

FME Server:

• Use FME Desktop to install your package.
• Find the Python site-packages directory
  
  • Windows: (FMEDir)\\python\\python27 (?)
  • Mac: /Library/Python/2.7/site-packages
• locate the directory that contains the init.pyc and main.pyc files for your package
• Open Web UI > Resources > Engine > Plugins > python > python27
• Upload the directory with the .pyc files.