Okay, so two topics.
Assenting: This is a sliding scale thing. On the one hand you shouldn't try to get everything your way, but on another you probably shouldn't play in a game that consistently works in a way you don't like. I was in a game recently, which seemed too focused on combat balance over player choice. I commented on it to the GM, and he made some changes, but it wasn't really enough. So I ended up leaving the game. I don't necessarily think the GM was doing anything wrong. The other players were having a great time. But it wasn't the right game for me.
So, assent if something is below your threshold. Comment on it if it is not, and try to reach a compromise, or a situation that is outright better for everyone (maybe everyone would actually prefer the second timeline). And stop commenting before you reach the asshole threshold where you are lowering the others enjoyment to raise yours. At that point you either need to decide that you didn't care that much anyway, or find a group that better meets your needs. (Which might end up being the same group playing a different campaign or rulesystem)
Timelines: I definitely prefer the second also, but there are also times for the first. But the second by default, definitely. Thief wants to use Disarm traps? Sure, okay. "But what do you do?" Another way to look at the situation (instead of fictional vs real timeline) is that we are looking at a mechanics vs fiction issue. The Alexandrian had a blog post about it just a few days ago:
http://thealexandrian.net/wordpress/37976/roleplaying-games/art-of-rulings-part-3-the-fiction-mechanics-cycleSo the thief starts of by implementing mechanics, and after the check the GM comes in with the fiction. Usually I'd want the thief to provide fiction also in these cases, but in this case it might actually be hard, since the player doesn't necessarily know what would work for disarming wards in this setting. So it is up to the GM to provide the fiction, or at least help with that.
Thief: I've got a move called Disarm Traps. Can I use that?
GM: Sure! Roll +Dex
Thief: I succeed
GM: Okay, so you pull your divining rods out from your kit of thief's tools, and disrupt the magical aura around the ward for long enough that you can smudge out part of the rune without activating it.
or maybe
Thief: I've got a move called Disarm Traps. Can I use that?
GM: Yeah, sure, you know how to disarm magical runes such as these. You need to smudge out the rune, but first you need to disrupt the magical aura. You've got some gear for that in your thief's tools.
Thief: Okay, I pull out the necessary tools and try to disrupt the aura. And.. I succeed.
GM: Okay, so you manage to disrupt the magical aura around the ward, and then quickly smudge out part of the rune.
But I wouldn't respond well to "Oh you know... we'll figure that out after we see how the roll comes out." either. That's the real sin as I see it in this situation. The GM should preferably have at least an idea about what is happening in the fiction, before the roll. Otherwise he has no idea whether the thing might be possible to begin with. And if reality depends on the dice rolles, then player choice loses meaning, with everything coming down to whether you have the right moves and manage your dice rolls.