I see Sparhawk wants to disable the warning sound alone and not the popup. I stumbled on an xposed module which will disable both. I just keep this posted just in case if Sparhawk wants to slightly compromise on the requirement and also probably will help others who read this post.
Text from the post:
Disable the Low Battery Alert with Xposed POSTED OCTOBER 13, 2013 AT
12:30 AM BY WILL VERDUZCODIFFICULTY:1
Disable the Low Battery Alert
with Xposed There are plenty of Xposed modules out there. Their
purposes range widely from adding previously device-specific
functionality to patching bugs, and everything in between. This is, of
course, all made possible by XDA Recognized Developer rovo89‘s
fantastic Xposed Framework (thread) . The framework allows developers
to create a module APK that is able to make a modification at runtime,
while leaving original files intact. Both a boost in ease-of-use and
user safety, Xposed makes device modification into a click and reboot
A new Xposed module from XDA Senior Member defim has appeared, and its
purpose is to remove that annoying low battery popup alert that you
are given when running low on juice. Yes, being notified that your
battery is running low is generally useful. However, for those of us
who actively look at the battery meter in our status bars, it’s a bit
redundant. Furthermore, if you happen to be in a call when you receive
this alert, it will generally turn on your screen, thus reactivating
the touch sensor. For yours truly, this has resulted in accidentally
ended phone calls, unintentional muting, and more.
The module will work on any ICS+ device with Xposed Framework
installed. Simply install the module, activate it, and reboot. To tame
your low battery alert, head over to the module thread.
The exposed module is available in this XDA thread.
I happen to notice that with GravityBox You get an option to disable sound alone. The screenshot of that option is as below: