Is there a way to blacklist an individual application from using overlay-scrollbars?

I am going to answer my own question. Thanks to the user "SevenMachines" in ubuntuforums, I've found a way to disable overlay scrollbars for a specific application. I did a shell script with the following (for eclipse, for example):

#!/bin/sh
LIBOVERLAY_SCROLLBAR=0 eclipse

Then, make it executable, and using the "Menu editor", changed eclipse to point to the script.

Alternatively, in your .bashrc add the following

alias eclipse="LIBOVERLAY_SCROLLBAR=0 eclipse"

In fact, you may also want to add UBUNTU_MENUPROXY=0 so unity menus work properly with eclipse, so that becomes:

alias eclipse="UBUNTU_MENUPROXY=0 LIBOVERLAY_SCROLLBAR=0 eclipse"

[Note: that this will only take effect once you restart your bash shell]