Commit 8f9ff9f6fd4 to Spigot/CraftBukkit was supposed to resolve this issue but neglected to cancel the event in the method for native console users. That commit only cancels for remote connections.

The code executing the command is never halted even if the event has been cancelled here:
https://hub.spigotmc.org/stash/projects/SPIGOT/repos/craftbukkit/browse/nms-patches/DedicatedServer.patch#172