Minecraft – Remove blocks without logging in to the minecraft server

First of all, try stopping the quarry; if you can do it, it'll be much easier to fix it, since the items will despawn automatically. Otherwise, you can try to use MCEdit and remove the item entities that are causing the lag.

Only ops are able to program command blocks, so that should narrow the list of suspects. Some (virtual) face time with your ops should reveal the guilty party.

In the meantime, if your map doesn't rely heavily on command blocks, they can be disabled by setting enable-command-block=false in the server.properties file and restarting the server.

To locate the offending block you can render the world map showing just command blocks and redstone, using one of the many 3rd-party cartography tools. (I quite like Minecraft Overviewer for this use, and though it's not technically 1.4.6-up-to-date, it can handle Anvil and custom block IDs so it's still compatible.) This will give you a high-level view of the problem and let you zero in on the possible culprits. Compare it to a regular overworld render to find a recognisable landmark nearby, then fly/tp there, unearth it, and render it inoperable.