Ultimately, your 'justification' is just an assertion that if it doesn't come via the scientific method, either its not true or its not science.
I wouldn't call the idea that "Knowledge is good", wisdom is better than ignorance, and freedom is better than slavery, etc. counterevidence. But I believe they are true things which I cannot prove via any sort of experiment, in particular because 'good' and 'better' are of necessity subjective.
I don't think you can dismiss my line of reasoning by saying "ultimately" and then saying something I didn't say at all.
It seems that we indeed cannot agree on a useful shared definition of "true". The laws of physics are ultimately indifferent to our notions of truth, and yet our notions of truth are instantiated as emergent phenomena within physics.
I wouldn't call the idea that "Knowledge is good", wisdom is better than ignorance, and freedom is better than slavery, etc. counterevidence. But I believe they are true things which I cannot prove via any sort of experiment, in particular because 'good' and 'better' are of necessity subjective.