I'm honestly a bit surprised that they won't product change it even to the no-fee Amtrak card. I could maybe see some hesitation moving it to a standard BoA card, but odd that they wouldn't let you do it even to the AGR no-fee card. Sometimes, though, at least from what I've read on other BoA experiences, it could be something where it's agent-specific (some will and some won't.) I'd still call or chat in and see if they'd work with you on converting it.
I'll probably be considering this next November; somewhat accidentally my wife and I both got approved for separate fee cards from Amtrak. I wouldn't have done it intentionally, but having the 60,000 points between us will certainly be nice over the next couple of years. I don't think the benefits will work out to keep both long-term, though, but if we get good value out of the upgrades and companion pass we might still wind up keeping both around.