two things to consider here: what Masataka said was only what he believed, not necessary the truth. Afterall, it didn't look like Maya told anyone about what her true role would have been. Second, Souhaku was cut off from external connections due to Reiki. Sending ki into reiki literally meant send the ki to Nagi and let him "use" Reiki to kill Souhaku. But that wouldn't have been enough to annihilate the powers, "only" Souhaku and Nagi would have died then
nagi ask to masataka to kill him...destined to break the cog wheels, then he'll reborn clean(storyline jargon). now masataka said to aya b4 he said he love her, that he'll punch the 'harpoon'(sending ki), activate the swords power something that'll neutralize sohaku's power.......i dont think your explanation fits what i just typed.