I like touring bikes for the load-carrying capability, so my recommendations tilt that way. The Windsor touring bike (apparently the Fuji tourer with different decals) would be a sweet ride, but it'd likely need a trip to the LBS to get it built, adjusted, tensioned and trued. The LHT, if you get the ugly color, might be better for theft deterrence.
Panniers are easier to carry than the messenger bag, and easier to load with groceries and beer later. If you gt Ortliebs, you can carry them with you, so they won't be stolen.
If you get it now and ride it all summer, remember not to clean the frame. Just keep the drive train clean, and the bike will look old and dirty next to all the other bikes on the rack at school.
Invest in a good lock, and use it well.