It sounds like you were turned off by EY's illustrations with anime references, and not the actual conclusion of the article. In any case, I suspect you would have agreed with it had it been written about e.g. HPMoR!Harry's obsession with science-ifying magic.

It took me a (comparatively, compared to some other strangeness in the Sequences) short time to get past all of the anime references. I don't think that Harry wanting to science-ify magic would have been enough to bring me around, as what I don't like about the 'something to protect' post is that it seems to say that wanting to be more rational for small, mundane, and more importantly, common reasons aren't enough.

Not wanting to be ripped off at the car dealership, trying to find the best way to make economic profits, out-competing rivals, etc., are not sufficient for rationality, only a grand purpose like FAI or cryogenics or curing cancer or designing more efficient wheat yields like Borlaug are enough, otherwise you're just wasting everyone's time and should be content being a mortal.

From the article:

No one masters the Way until more than their life is at stake. More than their comfort, more even than their pride.

You can't just pick out a Cause like that because you feel you need a hobby. Go looking for a "good cause", and your mind will just fill in a standard cliche. Learn how to multiply, and perhaps you will recognize a drastically important cause when you see one.

But if you have a cause like that, it is right and proper to wield your rationality in its service.