Would this work?
Most commanders tell others not to toss siege. Not all the time do people listen though. Anet made a change where now it tells you what you are building so it is up to you to build the correct siege and not dump supply into troll siege. Before spamming F to build, read what you are building. Also sometimes others toss siege for commanders when he knows those players so in a way he may accidentally break siege that say his guildies tossed for him.
Like you said people will just tag up and break other players siege to troll either way.
You can report siege troller, and it may take time, but they will eventually do something g about it. With new players, send them a whisper, and suggest to them to mail siege to the commander, so they may place it. You may even need to offer a polite explaination to assist in educating them of the reasoning and benefits of doing so.