If PC-Speaker input is given enough filtering to make all those things that use sample playback over it you have cured the noise issue, at least from my experience.

You could also just let the signal go through a logic gate but that isn't gonna work with all motherboards as I have seen very varying levels in output, a lot do not do just buffered digital signal but already have some level of filtering applied and also attenuation. Window comparator + high gain amplifier should fix that but it is quite some extra components and also finetuning. Output will be as clean as your power suppy is with that arrangement.