All you really need to do it plug in the charger and after it starts charging stop bme (that's simply "stop bme" in a terminal as root), once you have stopped bme you have 32 seconds to change the battery before the N900 goes into autonomous charging mode (because bme isn't running), and once you're done restart bme ("start bme" in a terminal as root). The main caveat is that you need to make sure your N900 won't want to use more power than the charger will provide, so it is probably best to turn off GPS and 3G networking (maybe more if you are using a low power charger) before doing this.

Now if only I had a mini charger, say the size of a mini bluetooth dongle, that could provide a few minutes of power just to do this hotswap. One of those emergency chargers might do, but they're a bit bulkier than I'd like and I don't know how much current they put out.