Simple, activating the jump drive computer once will start charging it without needing to hold down the mouse button. No changes on power consumption or cooldowns if the power runs out, it will stop charging.
But we've got interior remotes for just such a thing :DOnly problem with logic control is that a computer controlled by logic loses its core link to it and then you can't place it on the hotbar which means you can't actually activate jump with right click with the current computer/logic setup.
But yes I would like it to keep charging after clicking once and even logic to start charging after jumping. Of course you would be responsible for the ship design to handle the power drain.