It's hard to respect someone who manages from their knees.
The trouble with going along and not making waves is that it leads to Enron and other organizations that were and are all about doing what pays well in the short term vs. what ensures longevity and what is right. Stealing from Customers - internal or external - is neither. The Customer for Life philosophy dictates that you always do what is right for the Customer, so long as it is within your organization's means. This doesn't necessarily mean doing what the Customer wants. Remember, every good compromise means that both sides get - and give up - a little of what they want.
But how do you deal with the scenario above, where a colleague or perhaps even your boss asks you to do something that you know violates that philosophy, or gets in the way of something else that is more important or more time-sensitive, without violating chain of command?
First, make sure your own bias isn't getting in the way. As much as we'd like to believe that we are independent and objective observers, it just ain't so. If you personally dislike the person who has put forward the new initiative, be aware that human beings have a very difficult time separating the message from the messenger (why do you think messengers hate to carry bad news?). Sit down and make yourself a list of why you object to the initiative, then read it after a good night's sleep. If you can still say you have solid reasons to object to the initiative, and it's not a personal vendetta of some kind, you're ready for the next step.
Welcome to the wonderful world of managing up.
Managing up essentially means managing your manager, and it turns on a very simple assumption: Your boss (or your colleague) is not a moron. If they are, you have bigger problems than the initiative they've put forward, and you really might be better off calling it a day and updating your resume. But if they're not, it's a simple matter of giving them a clear choice, just as you do when making an offer to a Customer.
Here's what to say:
"Just so I understand, are you saying that
If they say yes:
"Okay. So it's okay to let everything else slide in favor of
This is about when most people's brain starts working. They actually have to think about this question, rather than speak off the top of their head. A lively conversation is likely to ensue. But if they still want to go ahead, at least they're more likely to have assigned the new initiative the priority it actually deserves, rather than the 'anything to put out the fire' priority it may have started with. Plus you now have clear direction on that priority and what may or may not be permitted to slide to address it, which both keeps you from getting in trouble and showcases your skill as a tactical thinker.