I wouldn't think you should be that much slower on the same bike with gears... Certainly a few more sample runs are needed, but I'm a little surprised based on my own testing...

I've ridden the same 20mile loop once a week for a couple of years... over 1500' of elevation, and on many high end folders including my Airnimal Chameloen, a Reach Racer, a Moulton TSR-27 (and a TSR-9) .. the bike that surprised me the most was my 700c flat bar road bike with Sachs Two Speed Automatic (55/75 gear inches).. it consistently returns average speeds that are less than 1/2mph slower over the 20 miles than my fastest times on any of the other bikes... what does change is my average heart rate.. it is higher on the 2spd, indicating a higher average cadence at cruising speeds and more effort being expended up the hills...

I would expect your average speeds on the same bike to be about the same given your commute as you've indicated.. if that turns out to be the case, I'd run the single speed because of the zen thing .. elegant, lighter, less maintenance, no clutter, better workout.. and probably just as fast..