Compare the following two questions:
"If the energy in a computer ends up as heat and information, and the energy in a heater just ends up as heat, isn't there some loss of energy in the process?"
"If the water in a waterfall all ends up at the bottom, and the water in a hydroelectric dam all ends up at the bottom, isn't there some loss of (gravitational potential) energy in the process?"
One dumps all the energy provided into some sort of ground state as quickly and wastefully as possible, the other carefully channels it to extract an additional benefit on the side. The analogy isn't perfect (for one thing, the water at the bottom of the waterfall will land with more energy than the water sent through a turbine, and make a hell of a noise in doing so), but I don't think there's anything thermodynamically wrong with the idea of siphoning off and redirecting some part of a flow of energy to drive a turbine or a calculation, and still have it ultimately all end up as heat.