I too just started commuting. I have been biking for years, but what got me was biking under load. This is the first time I have biked with bags on the bike. It stresses the body in a very different way since the bike's weight and balance is all screwy (even with a perfectly balanced load, the arse of the bike is WAY heavier than normal). What does not kill you makes you stronger! You will get faster with time, and get faster quite quickly I bet if you can stick to it.

This experience has given me a whole new perspective and respect for bike touring and daily commuters who ride with loads on the bike. Kudos to you, especially if you STARTED biking this way. (Just think, you might do a recreational ride without all the stuff and suprise yourself with how fast you can go..)