You were in the correct place to stop. The first light is designed to hold back traffic so that the intersection doesn't gridlock and to allow traffic in/out of the residential property next door.
Given the low volume of cross traffic in the intersection, that makes sense.
First of all, don't let a loudmouth bully who's having a bad day (or life) affect your ride. F' *um! Use your best judgment and you'll be fine. Ride on!
I usually stop farther back, but often will go as far forward as I can and still see the light. I noticed that originally there was only one stop line before the building exit, but that at some point in the past year an additional stop line in the bike lane was added closer to Canal.
I get that! I'm actually coming from the SW and headed up to Chicago and Michigan, and ducking through the tunnels to St. Claire seems like the easiest and mellowest path through River North... But those first blocks of Kinzie after the river are pretty rough, it's true.