I grew up in SJ and lived in CH for several years. I agree, that avoiding the sketchy areas is difficult. (note to others: if the OP works downtown, there is no way to avoid sketchy areas). To the extent you avoid sketchy areas you probably trade it for high traffic. I think Admiral Wilson Blvd is your best bet, or ride to the PATCO Ferry avenue stop and take the train from there.

This is the liberal idealist in me talking, but I encourage you to take reasonable precautions and give it a go. Enough people doing this is the kind of thing that can make Camden a better place. By reasonable precautions I mean things like a generic bike, no Lycra, avoiding groups of people standing around, etc. Perhaps also vary your route and/or travel times.

Paul