Bummer, but you gotta do what you gotta do.

Folding bike in the trunk seems the best solution. Take lunchtime rides. There are some very rideable folders, with drop bars even - Bike Friday right in your neck of the woods makes some - and they show up on Craiglist now and again.

I don't think being multi-modal on the commute will work. That is a long trip to work, driving the whole distance is the only way you can hope to spend less than 3 hours/day commuting. But if an arrangement such as suggested above does work, that would let you avoid rush hour in Eugene - maybe there is none, but that woudl be my rationalization.