I'm wondering if it would be enough to start saying things like, "Okay, here's what your characters know about the situation, and here's three or four things that are relevant to what's going on, and here's 3 or 4 opportunities that are in front of you to affect what happens next."
Is this enough? Is this too inflexible? Do I need to be more open to player input? Genuinely I have no interest in pre-determining an outcome; I want the player's choices to matter to their fullest, but I do want there to be consequences.
I feel like I'm talking in circles now, so I'll hold my peace and wait for you, my esteemed colleagues, to respond.
I think after reading your post I'm as confused as you are, but I think you're honestly overthinking the situation.
Every action has some kind of reaction, but this isn't physics, that reaction may not be equal, and it may not be opposite. The "consequences" of an action may be positive. It's difficult to determine from your post exactly how you determine consequences of actions already....so I'll talk about myself instead.
Generally speaking whenever there is an opportunity, I will pre-determine some "costs" associated with those. Some of those costs will be able to be learned by appropriate checks by the players (though I may not mention which rolls they may or may not make to determine this). Some costs simply can't be known, they're too far out, they're too vague, they're highly improbable. Usually I'll make some behind the screen rolls as players go about their adventure, and depending on their actions will determine which costs become most apparent and immediate.
There will be an ever-decreasing skill-check possibility to learn of these costs until it effectively hits 0 and that's when those costs smack them in the face.
I'm not really sure how you're seeing this as possibly playing "Mother May I?" to some extent the players always have to ask the DM if something is possible, even if they're doing it via declaration. "DM, is this possible?" is effectively the same "I do the thing, DM tell me how it turns out." The DM must make a determination on if a thing was possible, how possible it was, and how successful, if at all, it was.
You player doesn't know what goes in to running a thieves guild. So he essentially has to ask you, the DM, how difficult it would be to accomplish the task and if accomplished, how effective it was. Perhaps the two of you eschew the dice and narrate your way through this. Perhaps you hold opposed die rolls to determine success or failure.
I don't think any of this is "Mother May I?" That's just a healthy negotiation between players who want as much as possible for as little cost as possible, and DMs who want players to have to work for their supper.
I dunno, maybe I'm as confused as you are.