Using the Option key works just fine on either handle or the on-curve node -- I use it frequently. The problem usually becomes obvious when I do something to the entire outline such as removing overlap or moving the entire outline a unit or more. Sometimes it would happen if I did a copy-and-paste of an entire outline, but I've learned to avoid that one by making sure potential problem nodes are changed to blue before the action.
I've been thinking about this a lot today, and I think the issues I'm having are solely because of the nature of the design -- the small round cornered connecting strokes. They are necessary because of the overall design though so it's just something I have to deal with.
At this point I think using Rainer's plugin as I mentioned above will be a big help in getting through this project because I can get a better match on the angles -- .5 degree or less. The small amount of displacement then, if any, would not be noticeable in use.