I think the cause is as much revenue-driven as cost cutting.

Sure there's some obvious cost savings of staff time and liability from cutting on interlining.
The OW airline who started all this is BA, a known scrooge acting more and more like a LCC, and the OW airline who's ignoring all this is AA, which although also a scrooge at times has still rolled out generous initiatives in cabin product and FFP.

However the ban on two PNR-interlining isn't universal - even BA will interline to itself (contrary to first information - wiki updated).

There are some benefits of this initiative to revenue.
This initiative penalises cheapskates who create their own connections but will not affect premium corporate travelllers who are more than less likely have the benefit of assistance from a travel agency and will book through bookings.
Furthermore it eliminates connections that work but (individual) airlines have not contemplated - it gives revenue departments more control over fares.