It almost seems like this could be described as dynamically building a per-user VPN, via inbound proxies for admission control and traffic src/dst filtering, and services hosted behind multiprotocol terminating proxies. Some extra client analysis (practically effective, even if no theoretically valid remote attestation), tedious but necessary work to understand the access patterns for all the internal services, etc.
It seems there can still be lateral re-infection via difficult to patch shared services (finance/procurement/obscure wikis). The examples in one of the papers (delivery people not needing access to financial systems) is completely bogus -- sometimes the worst engineered, most xss-y, mission critical apps have to be accessed by everyone, have insanely hand coded 'business logic', and no docs. Content aware behavioral profiling would seem to have a role in managing that risk.