The presumptive status of death is very different if one believes in an after-life from what it is if one does not. In the former case, death is rather like being sent someplace else, where one will continue albeit unable to return. Yet most people who ostensibly believe in an after-life respond to death as if it is a simple cessation.
There was perhaps good reason for Komachi to want to prevent Reimu and Marissa from killing each other. But, if the little girl dies, then she just goes someplace else, which is what people sometimes do as they remain alive. Would it be a terrible thing for that girl to cross the barrier and not return to Gensokyou? Is it a terrible thing for people to cross the barrier into Gensokyou and remain there? Is dying fundamentally different from crossing that barrier?