If you look hard enough, you’ll find courses like this on international sites/sites for English speakers:
The videos are supposedly in English, but the transcriptions are in English and Japanese. Similarly, the ‘Japanese Pronunciation for Communication’ course by Waseda University is entirely in Japanese, but with subtitles in other languages.
Otherwise… well, Khan Academy does sound like a decent alternative, but what I’d personally be worried about would be who exactly did the translations, and whether or not the way the teaching is done matches what one might find in Japan. I mean, even if the words used are correct, if the way things are envisioned is different, you might have a hard time getting your point across, especially since Khan Academy’s Japanese videos seem to be entirely based on translating the original videos with a new voiceover and Japanese text. Perhaps that will work out fine. Perhaps it won’t. I wouldn’t know for sure.
If you want courses from Japan targeted at a Japanese audience, I suggest you check this site out instead:
That’s their English homepage. I’m not sure if this applies for all videos, but at the very least, the introductory videos and preview videos seem to be YouTube videos for which you can get Japanese subtitles (uploaded or auto-generated).
Ultimately, it might be easier for learners of Japanese to start with something like Khan Academy since it’s easier to find relatively basic topics to study, but JMOOCs will probably offer a more ‘authentic’ experience.
Finally, if you want to try something that’s almost definitely approachable for Japanese learners, and you don’t mind if the content is a little kiddy at times, then take a look at NHK for School:
I tried watching their video about the Japanese Constitution (for primary school students, I believe) after about a year of Japanese, and I found it fairly easy to follow, even if I didn’t understand everything. (Full disclosure: I’m a Chinese speaker, so kanji and guessing when a new word is a kanji combination is rarely a problem as long as a similar combination exists in Chinese.) NHK for School provides subtitles in Japanese, and they even have a mobile app, at least on iOS, meaning you can use it on the go. (I don’t have an Android phone, but I’d be surprised if they didn’t have an Android app as well.)
I hope you find at least one of these useful. I discovered JMOOC thanks to this thread, so… well, thanks for posting this question!