How can I change the behaviour of the launcher icons so that they have their background toggled on only if the application is running?
I want backgrounds or borders highlighted if the application is active, like I have it on Unity 3D.
I am afraid you can't toggle the backlight of the launcher items in Unity-2D. It apparently is only available for Unity-3D and given the fact that most development has been halted for Unity-2D, I don't see any possibility of this feature being developed upon.
I got it! Thanks to the patch jokerdino linked, I was able to configure Unity2D so that it behaves the desired way.
I have prepared a script that applies required changes automatically. Therefore all you need to do is to download and run it.
Important notice: This script works only on Ubuntu 12.04. Because it patches Unity's files, use it on your own risk! Especially, do not force it to apply patches if it detects & complains it was unable to do it correctly.
The script will ask you for root password, patch two files and restart Unity2D shell.
To revert changes, simply reinstall package
Note: This change will be lost with updates. You will need to run the script again then.
Here are script contents: