You can log it as 0. It shows up as training during the week, but it doesn't count toward your weekly total. Then you can see how much biking you've done, but you don't have to include it in your hours.
Or you can choose a low gear and accelerate like a beast out of every junction causing a spike in heart rate, fatigue and sweatiness; then set your Garmin to auto-pause when you stop at lights so that you don't record any time that isn't spent exerting yourself.
It's still physical activity, and a lot better for you than the way I commute.
I second JJ - don't give up on logging it. Just count the L1+ bits or whatever. It's still physical activity.
When I wear my HR I count the bits where my HR goes over 120. Otherwise, it doesn't get counted. And I don't usually wear it when I bike to the grocery store.
I didn't know you could set the Garmin to auto-pause, will have to investigate (read the manual,...NO!)
Also Ian, you promised me a course file, yes?