I am guessing the teleportation pads are part of the zone and not an object? Are these some type of emitters in the zone that can be removed? Possibly an XML or ini file for the zone?

Yes they are part of the zone geometry and the emitters will be in there as well, however zone files are packed and to just remove the emitter would need to edit the majority of the elements above it as well due to the file structure. I also don't believe we have a program that can repack the files after the edit sadly.

I would love to see client mods, even simple ones like this, but that is a ways off still.

No worry.

I dont know if it helps, but Teleportation Pads are also a "city festival" item you can buy to decorate your house with.

And they work too. People have used them to break out of houses and use the entire zone the house is located in to create some amazing stuff.