That's pretty much it, Hayward. The only real way is to remove the commands, as the commands aren't changing. I was only recently taught how to do that item summoning bit as well, and it was news to me.
I used to allow the #zone command on my server, and when we first started out I had no idea that it allowed locs to be added after it. Well, my players sure figured it out, and I hated the way things went from there. This was back in probably April of last year. It resulted in a lot of lazy people. Trash mobs between bosses that never got touched. Monks who would tag mobs for the group and hit a #zone X Y Z hotkey to get back to them.
The only other viable option was #peqzone, but I never could get that working properly, and once I finally did, I didn't care for the fact that it would debuff the user as well. I wanted free and easy travel, but I didn't want people just going anywhere they pleased inside of a zone.
The solution we devised last month was thought up by my gal, and it would've been infinitely easier had I found trevius'
translocator script before writing it all up =P What we ended up doing was turning off #zone and putting an NPC in the Nexus who would translocate you to any zone that we had open on the server. (We're doing progression currently, so not every zone is open.) And, since we aren't even into Luclin yet, and to make people wait on spires would be silly, I added a Nexus Gate to the Kobold Skull Charm. Then, I made it so that each new character started with one in their charm slot.
Other than complaints about the recast time on the charm (which I eventually removed), it's been a huge success. Every class is able to get around, but they still wind up clearing trash rather than warping straight to bosses.
I know this doesn't address your main complaint (about the item summoning), but it was intended to show you how your players will do everything that you allow them, and the trick is to find a solution that restricts them to what you want. Unfortunately, that most of the time requires a custom solution that takes you a lot of time on your part. It would seem that to disable the command is the only way you can ensure it isn't used improperly, and that takes away from the sandbox element of the server that I know you want to maintain. I would wager that your server stability would drastically improve if you restricted that command, as you theorized.