I think this discussion has mixed up a long term NPC that travels and works with the party with a character that the GM has a personal stake in. I will readily agree that if the GM has a personal stake in the NPC, and treats them more like a PC than an NPC, there are many problems and issues likely to arise. However, it's also entirely possible to have an NPC adventuring with the party that the GM is treating like an NPC. I don't have any more personal stake in NPCs adventuring with the party than I do to any other NPC or PC. Since I have zero problem with a PC dying, and I roll in the open, it would be obvious if I favored any NPC. I don't.
I'm often of two minds about giving players NPCs to control. I will sometimes do this, but, over time, I'm slowly moving towards not doing it. And this is because I feel that the players already have an important job -- to advocate for their PCs. And, NPCs aren't just tools for a player to use in that advocation, they should have their own goals and motivations to create a vivid game. If I'm giving the PC the NPC, it should be with those goals and motivations, so actions can be chosen well, but that puts the burden to play multiple characters on the players. And, that's not a problem, players are capable of this. The problem really comes from having to advocate strongly for characters that might have different goals, or wildly different abilities. I saw this at the end of SKT, where the module encouages letting the players run giant allies, a few of whom have ulterior goals. This means a player might have to play an NPC in direct contradiction to their advocacy for their own character. This is deeply unfair, and runs into the same problems that many poster here are pointing out about a GM being invested in an NPC adventuring with the party. That moment really solidified some issues for me (and, if anyone's wondering, the player did a wonderful job of playing the giant's motivations, but it was at the expense of the rest of the party), and I'm much less likely to hand over anything other than simple NPCs (like soldiers or summoned monsters) to the players to run.