Why diode?, and is the voltage drop accounted for in such case?
The original NiCds, and NiMH's are rechargeable batteries, and are recharged by the computer when a reverse voltage is applied to them while the machine is on. Lithium batteries are not rechargeable, and can do nasty things when you apply reverse voltages to them.
Most clocks chips I've looked at, I've not looked at the Amiga, tend to work down to 2.2V or so, so its probably better to use a schottkey diode as they have a .3V drop, which gives you a bit more wiggle room on a 3V lithium battery. But a standard diode should be fine, it will just have a shorter battery life.