Here's the thing, though: you wouldn't include a hilariously incompetent computer programmer in a high-tech IT action thriller or New Media posthuman near future sci-fi. I mean, you might include an incompetent programmer - maybe the main character has some asshole foisted on him by politics or whatever - but the guy's incompetence would be taken seriously rather than played for laughs. It would get someone killed, or nearly so, or spell the character's own demise. For some reason, though, stories about magic don't take themselves - or perhaps it's the very premise of magic itself - seriously enough.
Again, I didn't see the usage of his incompetence here as being intended for humor. Since I don't agree with your distinction, your argument doesn't do much to sway me. I didn't see it as being played for humor at all, but for tension. I like tension, so I applaud this. Any of the librarians, or any of the other students, when faced with an out-of-control vocabuvore would try sorcerous tricks on it. He couldn't, so he had to find another way. He's not good at magic, but he's clever, and he used that to save everyone's lives. If he had been good at magic, and just blasted the thing with some spell or other, it would not have been as appealing to me. He brought a squirt gun to a Wild West duel, so he had to find another way to win, and he did. Yay tension!
I also don't really like the comparison of magic to computer science, at least not for this story. Part of the appeal for me was that the author went to so much effort to make at least part of the magic - the library itself - well, magical.
To me it seemed that the author went to effort to make it seem like computer science, but perhaps that's my skewed perspective. Particularly the gadget that Kas attached to the indexer to try to understand how it worked so that he could adapt it. That was straight-up reverse-engineering, and the way that Kas and the other experts discussed magic made it sound very computer science-y to me. It wasn't entirely comprehensible to the reader, but that's because we're seeing it through the eyes of Lazlo who is not much of a magic-user.
Which isn't to say that the magic here was entirely like code. There was an element of unpredictability that would not arise in code. But that just made it seem like a more dangerous more tense kind of coding (yay tension!).
Now, say what you want about how complicated and magical computers are - and how special it makes you :-P - but that machinery is still pretty explained to me. There are stories where the comparison would have been apt, but I don't feel like it worked for In the Stacks, and that's part of what I liked about it.
The most interesting things about computers is that, at the root of them, they are not complicated at all. They do exactly what they are told to do, following the exact instructions that they are given. When a computer has a glitch, except in rare cases of a short circuit or something, the computer is still following its instructions exactly, it's just that it's instructions were bad.
This isn't the first time that I've thought of magic-using as similar to programming because much of it is predictable in this way. The analogy falls apart the more the magic is random, but as far as the magic actually harnessed by the magic-users here, I'd say it's pretty accurate. And if you write a bad spell, then it might be like writing a bad program, the magic does what you tell it to, it's just that you didn't tell it to do what you thought you told it to do. Only the consequence, instead of a computer crash, might be a fatal accident or a portal to another dimension. The main difference that sets this apart is that the library is like a jungle of wild code that was never written by a user, and there's no real-life parallel to that. But that just makes it cooler.
Again, the comparison still worked for me for this story, mostly because of the way that Kas approached the problem of understanding the indexers. And hey, if you like the story because it didn't make you think of code, then who am I to try to dissuade you? But I liked the story partly because it did make me think of code. Divering opinions of story mechanics lead to united opinions of story quality.