... possibly highlighting the fact that those who outrank you may be making bad decisions or fucking it away, you are a jerkoff, regardless of the merit of your points, and in spite of your contrived eggshell-walking.
Since I don't know the specifics of "your friend's" story, this will be somewhat general...
In my experience, when things like this happen, generally, it's for one or more of the following reasons:
1) The "argument" that bad decisions were being made was poor. In short, they weren't supported sufficiently by procedure, publications etc...my gut feeling vs. your gut feeling...
2) The person making the argument was focusing on their own slice of a much larger pie.
3) The argument, despite not falling into one of the above pitfalls, was made in an inappropriate time, place, setting etc...Telling the OPSO the schedule is fucked up at the Friday AOM for example...
and finally, and this one is almost always present...
4) Not shutting up, saying "Yes sir" and moving on when your input has been heard, considered and disregarded. Fucking this away is what generally gets you labeled a jerkoff.
Just like with emergencies, there are damn few situations in this business which require "fast hands" and we know what those are. When I've thought that "the system" was wrong, I've always found it better to sit down, make sure I understand it and really think through my conflict before opening my suck hole...and when I do open it, to do it discreetly. Embarrassing someone won't help your point be heard either. After that, you've got to realize that sometimes things aren't going to go the way you think they should. You are at best, a middle level manager and sometimes you are just going to have to shut up and color. Don't have to like it...