I don't even recall them mentioning if Yu Yevon controlled Sin or not. I'd assume not seeing as it's a floating tick, and I would honestly be amazed if it was capable of sentient thought, let alone deciding to cause mass destruction through another living thing.

Really in the end Yu Yevon just sucked as a villain cause they never explained him or had him do anything except the back story through brining Sin back every time they beat him up.