A very difficult situation to be in, especially when the full effect didn't become clear until the flight was underway.
In that situation, I hope I would have said (in as friendly a manner as possible) "you stink of booze, are you sure you're fit to fly?", followed (regardless of the answer) by "lets call in sick, just to be on the safe side". Easier said than done.
I find it useful to ask myself the question "what's the WORST that can happen" (if I take a particular course of action). In this type of case, doing nothing might mean death (I did say the worst that can happen) whereas speaking up and refusing to fly might mean loss of your job. It's easy to see the better option.
It gets easier to say "no" as you get older/more experienced..... and that wasn't in any way meant to be a patronising comment......I'm just speaking from experience of the old age bit!