Right, I was thinking about this today, and I think it's a decent enough theory, so apologies in advance if you, much brainier people than I, figured out this already!
We all know that one of Mokona's secret abilities is to detect emotions, right? So maybe we over-looked a _very_ big Fye/Kuro clue in vol.4 in favour of one of Mokona's other abilities, his ability to mimick voices!
Crowd: *gasp*
That's right people! So in that infamous scene where Fye asks "do you want me to hold your hand?"Â and before Kuro has a chance to kill him, Mokona says "Kurogane is very happy!", maybe he's not just saying it to imitate Kuro, maybe he can sense that Kuro actually is happy...deep, deep down.
I know, stupid theory, but it made me squeal in Maths class, so it ain't all bad!