Actually it still makes sense because I'm sure he didn't want leaks to his retrieval of the Remover. If a soldier was left alive and reported it to Barcus or any other Zoalord, they would wonder why the situation happened.
And this happened when Barcus discovered Archanfel chasing Guyot, and he told the rest of the Council. This act help inspired the three rebels to investigate the Guyver, along with the fact that only Imakarum was allowed to deal with them.
If it went Archanfel's plan, Guyot would have kept his mouth shut or die, and even Barcus wouldn't have known a thing.