I am inclined to agree with you.
However I think the carrot on the stick for causing them to persist is maybe that with the Loganair partnership they can offer a more appealing product to customers - offering connections, and when travel further afield improves interlining onto long haul through MAN/DUB/EDI/GLA which is never something Eastern have done (what happened to their proposed codeshare with Aurigny...) Between the two carriers they would then serve most of Southampton's busiest routes, and be able to book them all via a single website (closer to what Flybe offered).
It is certainly a gamble though.