There needs to be a /wpremove
It removes the waypoint that you're looking at, which would be obtainable using the same method as /id
In return, it restores 3 lapis lazuli blocks back to the user's inventory because it requires 3 lapis lazuli blocks to create one
That, and/or allow moving waypoint blocks themselves, which would be useful as well: /wprelocate or /wpmove <id> (but make sure this isn't confused with /wpset <id>)
Ready. Go.