The OP's commute is harder and longer than mine. Mine is 32km, 1hr20min round trip and according to MapMyRide, I burn approximately 1,300 calories/day, which means that I can (and the OP can) eat more during the day to just keep up with the calorie output.
The other thing I wanted to say was that this past Sunday, I went on a 64km ride with a couple of significant hills and 1/2 the route was into a 25kmh headwind. My goal was to ride to finish, not ride to race, so if I had to slow down to 10kmh on some of the hills, I did so and I finished (3hr0min10sec riding time, ~21kmh avg) with some reserve in my legs (and a sunburn on my arms, LOL). I kept my cadence at its "normal" 80-90rpm whatever the speed and adjusted the gears to match. I never pushed hard, I paid attention to any pains in my body such as knee joints (I'm nearly 53 and I seem to have a bit of knee ligament issue, the side of the knees can get a bit sore), hip joints and calf muscles (they seem to be the ones that cramp most often). I also get off the bike and walk around for a couple of minutes every 20-25km which seems to help, especially after the first walk, it also gives me a chance to feed and drink. As I ride more and more and longer and longer, my strength will increase making it easier to ride longer, faster and harder and my aches and pains will diminish as the body adapts to the longer term stresses. I also remember what I read recently (was it Joey Bike?) about gearing down and standing on the pedals for a while to use different muscles, stretch out the legs, get the saddle-sore butt off the seat, all for a bit of relief.