It's better to think of axioms as definitions. If the axioms are inconsistent, it just means nothing satisfies the definition, which isn't the end of the world. People have spent time studying hypothetical properties of polynomial-time factorization algorithms, knowing full well there may be no such things if P<>NP.
There are models of ZF where the axiom of choice holds, and there are models of ZF where the axiom of choice doesn't hold. To "assume" the axiom of choice, is nothing more than to restrict attention to the former. No more controversial than, say, deciding to write a paper specifically about golden retrievers, rather than a paper about all dogs.