I think it's pretty clear they have gone for LTN purely because EZY are starting the same route. If EZY weren't moving I dare say FR would be doing CPH-STN.
With FR opening a base in CPH, they obviously see it as a good opportunity to try and push EZY off the route altogether by going straight into direct competition with them just as they move the route to a different airport.
EZY clearly thought the route would perform better at LTN than STN or else they wouldn't have moved it. That's possibly now not going to be the case. FR have a lower cost base and will probably price EZY out, like I think they may do to an extent with GLA and EDI.
The problem seems to be that FR is up for a fight, whereas EZY seem to have this mentality of quite quickly giving in and going elsewhere. As I say, EZY need to get a grip as and when FR penetrate into more of their routes.
RAK seems to be a good example. FR will operate from LTN 5x per week and from STN daily next summer. From 30 May 2015, EZY will axe their STN-RAK route. Could CPH go the same way?