If you know, a priori, refusing to work on something you consider to be unethical will have /zero/ effect on the overall project, but negatively affect you, is it then ethical to do the work, or are you required to fall on your sword?
1) Listen to all competing arguments. Make sure you are making a sound decision and your opposition is genuine and not based on a personal bias.
2) Make it explicit that you are are saying no in your role as a professional, and that this is not just a casual "no". Ethics require engineers to make decisions only in areas of competency, so make it clear that you are competent to make this decision, and your decision derives directly from your competency.
3) Write it down. The document should cover 2) above, and set down the defensible reasons why assent is being refused, addressing counter arguments. Consider that the arguments you write down could well be tested in court, and you will be cross examined on them. The document/report should be of the same level as if you were a consultant to your employer.
4) Sign and submit the document (keeping a copy for yourself). You need to be open about your opposition. Keep it at a professional level. Hopefully you will get some respect, as your document should make it clear that you have legitimate concerns and are not just being difficult.
5) Be prepared for the consequences. Your opposition is now in writing and impossible to ignore. No sane boss is going to ignore it, as the legal consequences of doing so are too great if you turn out to be right. You will have heat applied to you, as the alternatives are to either address your concerns or to get you to retract, and the latter option is cheaper.
6) If the final decision is against you, either live with the decision or resign. If the issue is of sufficient gravity your only option may be to resign, whether that be for ethical reasons or your own legal protection. (Yes your Honour, my work killed 100 people, and I was fully aware of it as shown by this document that I wrote.)
If you end up resigning, then you're probably making the right decision anyway, as the events leading up to your resignation will have shown your employer to be a dud.
Granted, reality won't be as cut and dried as above, and will involve a lot of anguish.
I think a lot of people flippantly say they would refuse the order, but it's easy to say that when it's not your neck on the line.
Truly a deep moral dilemma.
It's the worse kind of dilemma: the kind that people outside the situation will claim was easy.
Personally, I think the Zero-effect case should not be cast aside lightly. Pragmatism is a legitimate ethical model.