I've had some theories that seemed too awesome to be true in the past, but I didn't bother saying them for that very reason, but they all turned out exactly as I thought they would. So, I'll go ahead and venture this theory here. If that thing that Pain stabbed kakashi with is a chakra modulator, then you might imagine that it'll change some of the properties of the chakra. I suspect it can do things like change the opponent's elemental affinity. That'd just wreak havoc on their ability to fight. Might also change the type of jutsu user the opponent is. As in, if the opponent were originally more suited to genjutsu type fighting, they may now be more taijutsu oriented after the effects of Pain's chakra modulation.
You guys remember the Itachi/Kisame clones? That was Pain's jutsu that made them possible. It might be that Pain used the chakra modulator on Itachi and Kisame in a discovery capacity, to learn the properties of their chakra. He could've then used the modulator on the henchmen to turn their chakra type into the same as Itachi and Kisame's. Since they seemed to really be Itachi and Kisame, chakra modulation might actually be able to change the person entirely...maybe. That's my theory for the day.