No need to hypothesize about how it would work. Australia uses pen and paper for elections. It works fine.
(Aside: it’s actually pencil and paper since pencils are more reliable. https://www.aec.gov.au/faqs/polling-place.htm#pencils)
In some ways, but the ability to erase a pencil mark is a huge issue with ballots.
IMHO, pens with tamper resistant ink, plus a process for making an exchange for a new ballot paper in case of a marking error, is a much better choice.
The security is in how ballots are treated, how they are monitored and handled, not how they are marked. It's never a problem that they are in pencil. Ever.
If someone has an opportunity to monkey with the ballots? The system has already failed.
As I said in another post, if you think you found a hole, it's because you didn't research what's actuallly happening.