EZY might not be carrying as many passengers from SEN as they were before from STN but I'd bet they are probably making more money from them doing so. This is due to the fact that they have a monopoly there, are probably getting a very good deal from stobart and most importantly being able to charge more since SEN is considered to be fairly 'local' and easy for travellers. Flybe have a rather similar position at SOU.
However STN does still have some of EZY's less common routes (OVD, BIO, LJU, CAG) which I personally would have expected to see go before the more obvious BCN, ALC, FAO, and maybe these type of routes will become what the airport focuses on.
I don't doubt at all that EZY is a very well run airline and every decision they make is for a good reason but it does seem strange to publicly go on about expanding at STN and doubling the operation there only to go and cut it further a few months later, this possibly suggests the deal may have just been a bargaining point for LTN.