For example, I really wish LW could award karma to programmers for improving LW.

It can't? The programmers of LW should be incentivized to implement awarding karma to programmers. (Although I would deduct karma from whoever replaced the "Reply Permalink Edit" etc. with icons.)

Suppose PersonA did a ton of good work on Less Wrong and got 10,000 karma, and then donated all of that karma toward making some great project highly incentivized. This person has done two wonderful things - all the wonderful work and incentivizing more wonderful work - but they have 0 karma to show for it.

They have real-world karma to show for it. But if that isn't enough for you, they could instead invest their karma in the project, and get back some fraction of the karma voted to the project.