I think your reasoning is fundamentally flawed. For starters, passengers already have strong incentives to limit layovers (more time spent in transport and more exposure but also higher risk of disruption due to travel restrictions or flight cancellations). That would seem to reduce the pressure on airlines to do anything about it.
Importantly, the scenario you mention is typically not due to one airline artificially increasing the cost of direct flights through fees. What's often happening is that the airline flying A->C and C->B is not flying A->B but is trying to capture some of that traffic. They do that by being cheaper than competitors flying A->B directly. At a time when airlines are hurting for business, they have absolutely no incentive to stop doing that.