I had the same doubts in the last session we had. But the more I think about it, the less of a problem it is for me. Let me explain...
What helped me a great deal was the blog post 5 Simple Rules for Dating My Teenaged Skill System by the angrygm (it is a long but great read. Give it a chance). What stood out for me was Rule #2: Only Roll When There is Chance of Success, A Chance of Failure, and A Risk or Cost of Failure. Only have a roll when there are consequences. When the Players have time to cast Guidance, then they should be able to do so. If you do not want that to happen, put them in a situation where there is no time for it. e.g.
Rogue: I am going to pick-lock the door.
Cleric: I am praying to my god to support the Rogue in pick-locking the door. (aka. Guidance)
DM: Sure you can do this. But the Zombies are hunting you. You need to concentrate for a short period, during which they will catch up a little. Are you sure you want to do this?
On the other hand, when my Players are talking to a NPC and the Rogue declares that he wants to intimidate him, I disallow the Cleric to cast Guidance. Because in the situation, it does not make sense. Does the Cleric know that the Rogue wants to intimidate? Is there time to to cast Guidance? It is the same with the Help action. Is it feasible to help another player thread a needle? If yes, they can Help. But I would rule it is not helpful. So no...
Again, the angrydm explains it in a great way. Plan your rolls. Every roll should have a very good reason, else drop it. And then you can decide, in the current situation, if it is possible/feasible to use Guidance and/or Help. In the end, if you put them in front of a closed door and there is no urgency, they should be able to pray to the gods and help each other. The problem is, that it is a boring situation and you are missing urgency/consequences. Guidance and/or Help is only the symptom, not the problem.