First of all Jonas didn't and couldn't prevent Rogla to do anything riding like he did. Secondly the only thing Jonas could do, ridding the way he did, is to win the overall. That is on why he rode behind Rogla, knowing he is ahead in GC. It had nothing to do with protecting Sepp and his GC. Landa was the only one with that mission. Plus Jonas only came ahead in GC due to some shady team tactics. If it would be only about racing then Jonas would likely be out of GC contention in stage 1 already.
P.S. And as said, on how the team really feels about Sepp and his GC ambitions, we seen that after Rogličes departure. Sepp is now well protected by Jonas.