If you turn the layer to be scaled into a Smart Object first, you at least don't risk extra degradation as you go. Setting opacity to 50% lets you see what you're doing.
Anyone else?
Mylenium
Thanks for the help though. It's good to know when to stop looking for non-existant answers.
Set the upper layer's transparency to 50%, then activate
Image>Edit>Transform and drag the transform rectangle until point A is over
its target point. Drag the scale origin to the same location. This will
keep point A in the same location. You can then use the handles to rotate
and scale point B to match the location of your second target point.
For sub pixel alignment, zoom in. You cannot hide layers during a
transform operation, but you can use the layer palette to change the
opacity of the active layer.
That way you can drag the handles while still seeing the information you
need for an accurate alignment. The numeric fields may also provide you
with more accuracy.
It works beautifully. Great tip.