Because the Western Emperor is quite literally a conniving piece of shit, that wants to use her for his political purposes and self-satisfaction like how he'd use a toy to entertain himself, only that toy being an actual person.
The Crown Prince is actually drawn to her as a person because he's basically surrounded by enemies on all sides, even his best friend betrays him and his only sanctuary(his sister) is dead, so he wanted to have Marie(Princess Morina) to unite the people because of her character being described as saintly and possibly save him as well. She's been constantly displaying those traits all the time saving him(his soul in particular) and others from trouble.
For those who are going to bring up that he wanted to kill or torture her... You might want to consider this:
- A person accepted as a saintess by the people due to her deeds exists in the mind of the people, and said person is missing.
- That person later on appears.
- The current ruler is seen as a bloodthirsty evil Crown Prince, who wears a mask mind you, and has this imposing misunderstood, shut-in-himself strong aura of a tyrannical ruler. Therefore the favour shown to him is low, even if his deeds aren't evil his image is already claimed evil by the people because he brought forceful change to the status-quo.
- The Saintess rejects the ruler.
- The people now have a reason to stand behind the Saintess and oppose the ruler.
- Civil war breaks out. Many innocents die. All the blame is pointed toward the ruler(Crown Prince), his enemies increase, he probably gets taken out by being poisoned by his close aides looking to rise in power or other forms of betrayals. He dies. His vengeance and all reasons to take on the power himself, lost with him. The saintess gets forced to either marry someone to establish a new kingdom or gets taken by the West Empire. East Empire ceases to be shortly after. The people suffer, they all blame the former ruler, not seeing their stupidity and foolishness. Etc.
All in all, it would be a stupid ending to the country. He will lose his life, many people will die for nothing.
On the chance that he could stop this by taking her out early on, he as a Ruler of a country responsible for the lives of his people has to be ruthless and eliminate a possible threat to the future peace and prosperity. Blame him or whatever his decision is correct.