Listen, the elephant in the room here, which is not being pointed at, is the relationship between the House and the government. There comes a point when you can write all kinds of things on a piece of paper, whether it's standing orders or legislation, but if the confidence of the House in the government is not there, that's where the House goes if the government is acting in a way that is unacceptable to the House.
I appreciate that you'd say why go nuclear with non-confidence when what you're concerned about is something less than that. Well, that's your choice, but then you're saying you do accomplish something.
The parliamentary system doesn't allow for you to have confidence but not have confidence, have it and not have it. It's either you do and the government continues in office, or you say you don't, or you do something that by tradition amounts to non-confidence, in which case the government has to seek an election, and so on.
So the big elephant in the room--which I don't want to bring up, because I'm not advocating that this matter be looked at as a confidence issue but which nonetheless infuses a lot of this discussion--goes to the nature of the relationship between the House of Commons and the government. It's one of accountability, and ultimately it gets to the point where the House has to accept the government's actions, however distasteful they might be: you hold your nose and you're carrying on with confidence in the government, implied if not expressed, or you say no, you don't have confidence, and you know what follows from that.
There isn't any other way of penalizing or slapping the wrist of the government or whatever because they're not doing things that you'd like to see them do.