While Eastern has made some problems for itself, you do also have to feel for them. They are scrabbling about trying to find the biggest role they can have in a market where roles for people like them are fast disappearing. By no means at all are either all or the most serious problems (like bigger airports being less welcoming to small aircraft as they approach capacity) of their own making.
Taking on Loganair may have been fated to be a disaster, but it's one of few things they could try in a market where almost anything they might manage to make a go of would immediately be grabbed up by someone with bigger planes! Given that FlyBe has been a previous beneficiary of that, having a link with them isn't the most insane idea. And given that they carry so few pax a day, having their own reservations staff was perhaps a luxury they couldn't afford, while trying to market only their own flights was perhaps a headache looking for somewhere to happen.
There is a role for a respectable operator of small aircraft (ManxWing2 perhaps best showed the need and the opportunity), but it's a role that it is hard to carry out in isolation.