Not sure how you could silently say "amen"... You mean, in your head? God cannot read minds, because.... Well, let's just say that Santa is not the only imaginary being ever created from the imagination of men.
But you've got to pick your battles here...
I have said "amen" for a one-on-one prayer, and the person saying the prayer even admitted that it was odd praying out loud when they knew I didn't believe in it. But saying "I agree" (amen) was more out of respect that they believed in it, and didn't convey that I agreed with the RITUAL, or supported it, but did support the intent of their message. They knew that, so I wasn't just simply enabling their neuroses...
If it's a group who may not know about my beliefs, I bow my head out of respect, and don't close my eyes, don't say 'amen'. There's no point in being disrespectful...
I think of it as similar to standing during the flag salute: JWs don't repeat the words, they don't place their hand over their heart, but they also don't disrespect the pledge of allegiance: they just stand there, they just don't participate.