Bug, misfeature, whatever; it's a serious issue. It should never be this easy to lose that much data. Needing to hold F9 is a good idea, but it doesn't help if I think I've quicksaved recently but haven't.
PEBKAC is no excuse for bad design. Three Mile Island was PEBKAC. At the end of the day, if the game is ruined for me, it doesn't matter if it's my error that was the proximate cause. Good games (and good software in general) don't make these errors easy to make.
What differentiates KSP from most games here is that most games keep their quickload and their autosave synchronous - quickload usually goes back to the previous quicksave or autosave. Hence quickload never goes back farther than some sort of logical checkpoint, which in this case would be the launch. It's a subtle difference, yet it's crucial.
In the interest of constructiveness, I can see several solutions:
There could be a warning when F9 would load a previous launch. "Are you sure?" is a design crutch, but it would help (as crutches usually do).
F9 could go back to the latest quicksave or the beginning of the launch, whichever is later. Almost equivalently, the game could automatically quicksave at launch. (This may bite people who expect the current behavior, of course.)
There could be easy access to, say, the last five autosaves. This would be nice in general but presumably would need a bit more development effort.