Let's assume for a moment that the 6 destinations Flybe / Stobart chose to fly from Southend are mainly cities which do not have (or are about to lose) direct flights to SE England. This implies that these 6 cities do not have enough demand for a B737 / A320 from London.
If a route from London cannot support 150 pax per day, it seems very likely that demand for connections via Southend to/from Carlisle is likely to be very small. I just can't see many people wanting to fly Carlisle-Munster for example and would expect those travelling to/from Manchester or Glasgow would likely pick a route from MAN / GLA to an alternate airport instead.