Hold it now. Axia are not derived necessarily by any means, although they can be derived by some means if you want (statistical studies, etc). They are simply a basis by which you will apply some logic.
I have never heard of any school of thought that assumes you axia are not true. Why choose an axiom that isn’t true, or I should say that you don’t intend to assume is true? I have this mental image of my modern algerbra professor standing before class, writing down some assumptions, doing some formal logic, then after we had written everything down stating “Now, I will assume this axiom is false, which means you wrote everything down for nothing. Ha ha ha ha!!!” … actually that sounds like something he would have done. 
Now, this isn’t to say when you are done with a particular set of axia, you cannot go back and adjust the axia, including adjusting one to assume it is false or negating it. i.e. if in case one A=B, you can then have a new problem where A<>B. But this is a new problem completely distinct from the previous problem. But I cannot imagine coming up with a problem, in which, we will assume false axia.
I agree that a counter-example to a conclusion is silly. But a counter-example to the conclusion by any logical means is silly.
For the inductive case,
#1)Axiom. I know some CEOs that make over $200,000
#2)Logic. Inductively, all CEOs make over $200,000
#3)Conclusion. Therefore Mr. Stone, a CEO, makes over $200,000.
The counter-example, Mr. Glitch who makes $80,000, refutes #2 not #3. It is not a counter-example to the conclusion but a counter-example to the logic step.
Sure I can based on the axiom which is assumed true. As you already know, you can take faultly axia, apply proper logic, and reach a logically true, but real life false conclusion. The deductive logic in that case is perfect if I assume the axiom that all CEOs make more than $200,000; however, by providing a counter-example to the axiom I show the entire proof to be wrong.