"I understand why you want me to spare him, but i still think there is no difference in what I am about to do to the city and me sparing him".
A city of ten thousand population getting destroyed is sure to attract attention, the church Included.
Him killing the Emperor or not is not going to change anything about him being a target and being sought after.
What will be different is the motivation that led to the church dispatching their investigation unit.
[ You are right. It is the same, but there are also some slight differences ].
The destruction of a city cannot be compared to the death of someone who rules over a lot of territories bigger than what a ten thousand population city is capable of.
While it would still render someone asking questions, there are ways to prevent that question from leaving a trace directly to Sango.
The destruction can be covered under the guise of an Ebora or an Agun involvement.