[Muromec]

>Can activists organize an election for all citizens of that country in some online form, asking the voters to scan their passports using their phones, so that

By the point said activists reach organizational capacity to do so, they have already won and can hold the vote basically with scanning a qr code with a simple app.

>only legitimate citizens (who have passports) can vote

this makes no sense as a requirement in a situation you described.