There are certainly some areas of the Williamette that are not conducive to paddling (especially at night) and I'm not sure you could safely bypass Oregon City, at all. This milltown with its waterfall in the center of the river will, I believe, be only passible through the locks.
There is a photo on google earth of paddlers near the lock gatess, so I guess it's possible, but you aren't going to get there safely by floating aimlessly at night.
There are also lots of floating obstructions on the river at verious points. Bridge abutments (left behind after the bridges were destroyed), logging debris (probably lots of that in the water), and other construction artifacts which may be an issue, depending upon water level.
Not saying that it can't be done, and you probably know the river better than I, but floating aimlessly at night on a river with boat traffic, lots of which is logging traffic, isn't a very attractive proposition to me.
EZ-Dock modular docks
Kayak Motor Kit
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