It absolutely does not use blindness as a stand-in for incompetence, that is your own outrage-seeking interpretation of it. A neutral interpretation would be that "flying blind" is to "operate without perfect information". It is a simple description of operating conditions, not a derogatory term in any way. Your reply is worded in such a way as to indicate that you think the person you're replying to deserves to be shamed for 'defending' it, but having a disability does not entitle you to browbeat the world into submission and regulate all usage of any words associated with your disability as you see fit. This is quite benign and people are perfectly well within their right to object to somebody trying to police plainly descriptive language.

You are equivocating. Blindness as a personal chronic medical condition is not the same as a situational difficulty.

The pilot who is "flying blind" has perfectly normal eyeballs. They are not necessarily a member of any minority group, except for their chosen profession.

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As for "blind" being a word that appears more frequently in a negative rather than positive way... Well, I'm not sure what to tell you, that's just 10,000+ years of language from a species that evolved to prefer seeing.

To offer an example of the positive case, the idiom "justice is blind". Yes, there is a popular cultural mascot wearing a strip a fabric over her eyes, but again: The justice doesn't actually involve any (real) personal medical condition, and it's considered a positive feature for the job.

Well flying blind is unsafe guessing (ignoring modern instruments), that's a fact. But only "flying" and "blind" together. No one thinks this makes the word "flying" has a negative connotation here, and same with "blind".

Like "drinking" and "driving". On their own, they're both neutral, but "drinking and driving" is really bad.

No, it means not being able to see what is going on. Which is literally what the word blind means. You can be blinded by many things (blindfold, clouds/fog, bright lights, darkness, accidents, genetics, etc), permanently and temporarily. Non-humans can be blind and blinded. YOU are making it about a specific situation and projecting value judgements on it.

The author specifically says FLYING blind. Not "stumbling around like a blind person" or some such. If you are offended, that is on you. It's your right to be offended of course, but don't expect people to join in your delusion.