its already closed and been addressed. hence why there clear cut warnings now in using it. (because not everyone codes their plugins to handle it)
Please don't remove this command, developers can't do anything without it. Well, I can't. 
Warnings + name and shame in crash reports have been added
The problem if there is an flag that adds it back stuid owners will always add it.
I think instead we should add a message on reload that they shouldn't ask for support if they use it. Also remember that server was reloaded and print that at crash reports too to indicate that user shuold solve the problem himself.
The usual argument against removing /reload is "many developers like to use it".
But i think you are right, it would be very convenient, if there was a "debug" option in spigot.yml (or bukkit.yml) to disable this command on live servers and keep it in test environments.
Well even more of a better way to disable is have it as a spigot.yml setting, so it would be possible to disable it even without any permissions handler plugin. Its just known to cause serious issues, is only plugin friendly when a pluging explicity is coded to handle it (and not alot are) Granted maybe some experience server MC operators would know when it is or isnt safe for them.
Developers often use /reload, and what your suggesting is easily accomplished by setting bukkit.command.reload to false or -bukkit.command.reload with your permission manager.