Sephiroth1999AD has the idea here.

Since Yuna developed a bond with the fayth of the aeons she got, Yu Yevon would have the access to those aeons when she was around, I think.

The fayth keep telling her "Call us!" They realize that if she summons them before Yu Yevon inhabits them, then Yu Yevon loses the aspect of surprise, and she will be more focused and able to defeat them. When using the Final summoning, not only have you just lost your friend, but generally summoners only have a few guardians with them, and the battle against sin would be more exhausting without 7 people fighting against it xD

then there's also that yuna and Co. are far more powerful than any other people in spira have ever been, thanks to long hours of spherewhoring.

anyways, the fayth in themselves are not evil, it depends on who tries to use them