A lot of commuters don't use clipless pedals. I used them for a few years then switched back to plain pedals and prefer them. I can wear any shoes I want, rest my foot on every curb I stop by without the nuisance of clipping in and out, and most people don't commute at race pace.

Since you have a lot of hills and a sketchy knee, remember to use a lower gear and spin at a high cadence, rather than using a higher gear and "mashing" at a low cadence. Spinning is easier on the knees.