Can a collaborator delete a branch or the whole repository in a free Github organization account?
For branches: yes, if they have been given permission to do so. Entire repositories: no, since you need to be an organization member with appropriate permissions - and you seem to be talking about collaborators (which is a per-repository thing, a collaborator does not have to be an organization member).
Thank you for your reply.
What what is the best way to protect a branch from deletion and push events for a free organization account while working with organization members or collaborators?
Developers should be able to read, create new branches, and making PR.