i agree that empress' little game is brutal but i think in her own way, she respected johan and may even have had some sort of friendship or allyship in the past with him, given that the emperor and her brother was best friends with him. i tried to interpret her putting shuri in a tight place as a way to ensure that johans children is in the right hand and that the family may survive until after jeremy takes over. i can always be wrong though, as for now the empress doesnt seem to have any serious motivation other than boredom and politics to possess a personal threat to shuri, but she may have that reason in the future.
for the church, IMO, theyre not black and white as in theyre going to be bad. at least cardinal richelieu shows to be a very grey character, i cant say the same about the church
the empress doesnt have ill will against shuri, she was simply making this spectacle to see how she deals with political affair. think about her trying to proof her worth in the council earlier, or when she organized the memorial party, this trial is like that but the only one shuri needs to impress this time is the empress without shuri even realising shes playing a game. yes, the empress is wicked and cunning, but is she evil exclusively in relation to shuri and jeremy? no i think not. she might have had her pride hurt when the emperor chose theo's mother as his first wife, and she might have a vendetta against her, but as we all know, shes dead, and the empress is bored, along came shuri.
i actually quite like the empress as she has shown to be very level headed and looks like a good politician but also has a mundane side.
as for theo, like shuri, hes practically a child. both theo and shuri shouldnt have been put in the positions theyre in now (crown prince and interim house head). the fact that he has a deep seated mommy issues is not his fault. hes manipulative and most probably sociopathic, but the adults around him are gullible and faults lies with them not him.