Sure, you could enjoy the company of the annoying sidekick character. It's an acceptable thing, unlike pedophilia. It will work on a mainstream level, too, OoT paves the way with rave reviews.
The thing is, it doesn't enhance any of the things that games do really well. Developing a sidekick character like this only imitates workings of other media, and mostly produces a poor imitation. If you're a true game designer, not just a person out looking for money, I think you'll focus on the interaction of a player with the world, including its characters.
Yes, you should be able to part company with that fairy, maybe even hurt her feelings or crush her into narcotic paste. If you like Navi, then you'll like her even more when you keep deciding not to end it. That would be much better than, "Do you want to listen to Navi? No? Too bad! Maybe you'll learn to like her in the next few hours." The thing where you can't change anything, that's what books and movies are for.
The only way the fairy should be associated with the Z-targetting system is if you can play the game without the fairy and without the Z-targetting. And I would. Especially if pressing the Z button still allowed the leaping attack.
But all this, the entire article and follow-up, ignores the real problem. The Exposition Owl must go down.
The hatred of Navi is one of those wonderful things that start out as something that people smile and nod about and after a thousand gamers repeat it people start to draw Link killing Navi.
But she was annoying. "Hey, Link, I bet those Iron Boots would be great if you needed to walk at the bottom of a lake!" No shit, Navi. The bottom of a lake, you say? Like this one I'm in the bottom of? You know, I could maybe find an entrance to a dungeon in here, such as the one right in front of me! Aren't you helpful.
In my particular case she reminded me just as I was entering the Water Temple. I walked inside to shut her up. (The water temple, conversely, isn't so bad, and if someone told you you can get stuck there if you save at the wrong moment you're wrong. Go train your 3D spatial perception, peoples.)
Her biggest problem was that she went against the spirit of the game. Zelda is a game about exploration, about finding weird stuff under rocks and in the middle of cabbage patches. Every time you get a new way to get around you go find all hindrances that are no more. But Navi always assumed you were lost. You poor thing, are you looking for the next temple in this cove? No, there's just a useless heart-shaped crystal here. This is the direction for the next temple, here!
And of course you had to either indulge her and stop gameplay for a moment or keep listening to her shrill voice, so it's a lose-lose situation.
It's curious how they tried to fix it with Tatl but I guess her 'tude only bumped her from 'annoying' up to 'forgettable'. Tatl only comes in conversation as a comparison to Navi. Poor thing, she's worse off than a sidekick.