Eventually I was dismissed from this company a couple of days later and this situation was raised as one of the points. I was told "you can't refuse a mission given to you by your manager, regardless of the circumstances, that's ridiculous" and when I replied "I have different views to you on this" it was considered to be rude. The person who dismissed me is more or less the management boxing bag - a certified "yes man" who nobody respected.
Of course this hasn't changed my attitude, though. Still a proud "no man" and wouldn't go with the flow unless I'm sure everyone completely understands the consequences. At some point people have to realise that their loyalties don't go towards their manager and instead should go towards the shareholders and clients. There is a bit of give on this, of course, but eventually you have to do the right thing by the people that actually stand to gain and lose - not just being another cog in the machine that exists only to support other cogs in that machine.