Some of the provided examples I would consider to be "badly played," but not necessarily "bad." For example, instead of just straight-up saying "You're intimidated" (which is horrible DMing, IMO), I'd frame it as a behavior the guard engaged in--probably without telling the player that I was rolling at all. For example:
DM: "Things are not going well at the town gate. Dwarves aren't well-liked in this settlement, and since you adventure with one..."
Elf PC: "I speak to the guard. Sir: I swear to you, on my family honor, that this woman is an upstanding member of the community who will respect all the laws of this land."
DM: "The guard looks from your face to hers, then back to yours. Finally, he stands very straight and approaches you [the elf], leaning close enough that you can feel the heat of his breath. You hear the sound of his sword sliding a few inches out of its scabbard, and he says, 'The dwarf can stay outside in one piece, or she can come inside in two pieces. Take your pick.' From the battered look of the man's armor, you can tell he's no stranger to combat, and he certainly looks like he could back up that threat."
Dwarf PC: "Maybe...uh...maybe it would be better for me to stay out here, for now, guys. If that's okay with you?"
Elf PC: "You have made an enemy this day, sir...what was your name?"
DM: "He says his name is Errol."
Elf PC: "Sir Errol, you have made an enemy of me and my house this day, but we will abide by your...restrictions...for the time being."
DM: "Errol sheathes his sword and says, 'See that you do.' "
Nowhere did the numbers or skill names show up, but the guard pretty clearly made an attempt to intimidate the party. For a low roll, or against a character that was known for being belligerent and winning fights, I'd narrate it differently--might say all the same stuff, but add, "Despite his bravado, you feel like you could take him if he tried something." Or might say something very different. I dunno. I'm not really a DM myself.
Basically: Show, don't tell. Show how the NPC (or hell, even the PC) intimidates, deceives, or persuades the party. Each and every one of those aforementioned things COULD have been done by a sufficiently-savvy DM spinning things properly.
Edit:
Maybe a better way to say this is that I don't have a problem with skill rolls influencing behavior, but I want that influence to be explained. Leaving it as "NPC rolls X, that beats your Y, therefore you are Z" is just painfully bad storytelling. If you're using these rolls--presumably, to determine which direction the story goes when you don't have a particular idea in mind--then it should be as a guide to how you address the situation. "Intimidate" doesn't automatically make the opponent afraid--but it may make them an enemy. "Persuade" doesn't automatically make people like you--but it does make your ideas sympathetic or attractive in some way. "Deception" doesn't mean people believe you--but it does mean that even if you've told them something false, they might act on it. Leverage that leeway in those skills. Intimidation might make the PCs back down out of fear of force...or it might incite them to attack. Persuasion might make the deal sound sweeter than it is, or lead to the addition of extra "fluffy" benefits which might be interesting down the line (for the stated "I don't wanna quest for just 100g..." example, perhaps, "If you do this quest for us, we will formally grant you a title in the Court--ceremonial, of course, but with some attendant privileges and access to <resource the PC might want, e.g. Royal Library or Militia Armory>.") Deception might give the players a half-truth, or put you in a position where you can imply something or let them draw a false conclusion and then "confirm" it with the NPC's testimony.
It's not *easy* by any means, but this is the kind of thing you really have to do if you're going to employ these "rolls" against PCs successfully.