Looking at the code by which footer is inserted, I believe it’s not possible to insert JavaScript via Footer and Top.
The only sections which supports injecting JavaScript are Header, </head> and </body>.
I am not able to repro this, normal content appears fine in Footer. Also here is one of our hosted instance which has custom Footer:
http://forums.mtbakervapor.com/t/welcome-to-mt-baker-vapors-discourse/6
Looks just fine.