One of the fundamental ways category theory is used is to define categories of structures, where the morphisms are structure preserving maps. E.g. the category of topologies has continuous functions as morphisms.
But as far as I know, this is just a customary way that category theory can be used. We could just as well have said that the category of topologies has all functions as morphisms including non-continuous ones.
This would of course be useless, but apart from its practical use, is there also some sort of principled deduction that “structure preserving maps as morphisms” is somehow “the right way” or “a canonical way” of defining categories?
Category theory doesn't really care about the structure of its objects and morphisms. For instance, the category of topological spaces is made up of all topological spaces and all continuous functions between them and at that point the category theory stops caring about what the objects and the arrows are. Just whether they exist, whether certain compositions are equal and so on.