Is the crazy intersection/bridge you're talking about the BU bridge, or is there another bridge on #1? I lived near the BU bridge 30 years ago, and it was heavily traveled by bikes and not considered scary or out-of-the-ordinary for city commuters. Guess it's a matter of what you're used to, but all the BU, MIT, and Harvard students bike through there all the time, so you certainly wouldn't be alone. At that intersection, it's safer to stay to the right and make a left by crossing the intersection twice with the light, then stay on the sidewalk over the bridge.

Your #2 route is through pretty areas with lots of hills as I recall, and the rush hour traffic will be moving fast. If the shoulder is adequate that should be a nice ride, but if no shoulder and a curb it could be scary.

Do what you feel safe and comfortable doing, but I can guarantee that your comfort level will change over time. Just see what the other cyclist are doing and go with the flow.