The Cougar’s problem is more about Baylor than BYU. The Big 12 has been embarrassed by what happened in Waco, and the harassment of Title IX victims. BYU has had similar issues related to victims of sexual assault being investigated and/or punished for violations of the school’s honor code, and the Big 12 wants no part of that.
For their part, BYU has told the conference that the honor code will be changed in two ways. One, to give amnesty from honor code violations to anyone reporting a possible Title IX violation, and two, BYU has promised to revise the honor code to not discriminate against LGBT rights. However, promises just are not enough. The Big 12 wants to see the changes publicly announced before making a decision to invite the Cougars.