In season 2 Dexter still found it hard to connect to people emotionally he has grown a lot more since then and learnt to treasure his connections with people.
Debs, Rita, Lumen, Astor, Cody, Harrison - to an extent Sonja!
Back in Season 2 when all this was threatened he barely cared for them, it was a disguise, with the exception of Debs. That is the difference - Dexter has grown since then, that's the whole point! GROWTH!!!
Back then Dexter just didn't want to be caught. In this situation Dexter tried to make sure that everyone he now genuinely cares about was far out of harms way before he attempted to deal with it.