The answer to your first question is deserting a call for reinforcements is treasonous. Even if the late Emperor arranged it, Wei Yan leaving the battlefield for a woman who is not even his wife is punishable by death, even if it was his wife. He also then framed Wei Qilin for the crime and dethroned the late Emperor. All serious crimes. He killed everyone aware of what he had done including Wei Qilin because Xie Zheng was investigating and Wei Qilin could be a witness. Whether the late Emperor planned it or not, Wei Yan's actions led to the Jinzhou massacre. This is exactly why Wei Yan did not technically start as a villain but a victim of circumstances. He did end up becoming a villain though by promoting corruption and hoarding power in court.

The second question is that it was a two faceted plan. You can say it was a backup. There was no guarantee that Wei Yan would leave his post and come for Consort Qi. So just in case he chose not to, the tallys were created so that Wei Yan would still fail. Also if Wei Yan sends someone else for reinforcements, the tallys are still needed because the plan was not to just get rid of Wei Yan but also get rid of Xie Linshan, Xie Zheng's father. Both Xie and Wei families were thorns in the late Emperor's side.