I'm definitely not one to ride in those areas, but I would also choose #1. You can always get off and walk across a scary intersection as a pedestrian, and as others said, there are tons of commuting cyclists on part of that route.
You will get to know the traffic flow, etc pretty quickly. My son, who is not really a cyclist had some car issues last week and his boss gave him a bike to ride to work. He lives in JP and rode to Cleveland Circle and also around Boston, Cambridge. He found out he really likes riding, so now I guess we're a 4 person cycling family! But, he quickly found out what intersections were scary and how to by-pass them. Be careful, but enjoy!