I am an admin on a busy whitelisted server and on occasion we have to use commands like xu_killitems to clear someones messy setup.

This causes the Terra Shatterer to also be removed. You can imagine the annoyance of losing your S nearly SS TS.

Maybe if you could place it in a container whilst charging it would alleviate the issue

The issue is with the fact that you have to kill items. perhaps limit total items on the server?

That is not really an option for bigger (or even small to medium) sized servers, unless of course @yrsegal you have an easy forge based way of doing what your suggesting?

Or, you know, broadcast an announcement that you're going to use the command. If it's YOUR Terra Shatterer, then just pick it up first.
Alternately, if you have ClearLag, is has a /lagg area command for destroying all entities in a specified radius instead of simply everything everywhere.