It is very nice that they chose to display this coin. Please don't make them regret it. They are likely doing so as part of an exhibit on the history of money, not because they want to use their good name to endorse Bitcoin. If their choice to display it comes with a paparazzi, or a perceived legal or accounting burden (the same way if I mailed a coin to the EFF and put the address in a forum post that said "look everybody donate to the EFF through this coin") or they start to feel like they're being made into a billboard, the only thing that could do is motivate them to take it down.
I think they should even put a little live-display below the coin showing the balance in real-time.
They put it on display and bitcoin is something refreshingly new amongst all these old silver coins. Why hide that fact?
This coin is alive!
I don't really share your concerns. The value of other stuff in their collection probably changes over time, too. I honor the fact that you donated the coins to them and will follow your recommendation and not send any MORE donation than I already sent and I will not pester them with more emails. After all, you made this happen and I don't want to risk spoiling it.