I think you are right, however prepositions are quite tricky for those whom English language is not mother tongue.
In Polish we could say "on": eg. "12,428 people have now died on COVID-19".
I don't think that was GP's point. "From" seems absolutely correct. Using "with" would mean that the number refers to people who died while having COVID-19; using "from" means COVID-19 was the cause of death.