How can I determine whether rust has made my bike unsafe? I ride a 1972 steel frame bike year round through Canadian winters.

When I got the bike it was in good shape, but after putting a few thousand km worth of commuting on it, it has a lot of scratches in the paint - mostly from things like road salt getting kicked up at speed.

In the course of the last winter, despite my best efforts, many of these spots started to rust. I can remove most of the rust spots with careful application of steel wool, but I'm now a little worried about the structural integrity of the bike. I notice some creaking when I shift more of my weight to the bars for instance.

How can I tell whether a bike with some rust damage is still safe to ride on?
Sounds like you have only surface rust. The frame would have to rust through to cause any integrity problems and that would take many years of damp conditions. The creaking you hear when shifting your weight to the bars may be the headset. 

It may be worth getting it serviced. As its likely the grease has escaped/become clogged with dirt causing the creaking. It would be wise to check all the joints and welds for signs of fatigue or cracks. Ensure they are all solid.