Well, he does confess that he'd wanted to kiss her/be intimate with her for a lot longer than he'd like to admit so he'd probably been silently lusting after her for months by that point but was trying to ignore it since he's got a job to do, plus his head mess, the lyrium withdrawals and everything else.
In regards to Haven, I think at that point he doesn't expect anyone to live, even with that secret tunnel. It was a chance they had to take and the Inquisitor was really the only one who could stay behind because the attack was directed at her. Plus, at that point they'd all assumed it was mainly just a dragon and an army led by Samson/Calpernia, so when Corypheus showed his face they were likely all cacking themselves. Cullen's also front of the pack when they find the Inquisitor as she passes out in the snow (likely a coincidence), so when we do finally get that Skyhold scene where he starts to make his feelings clear he seems relieved to get it off his chest.
Also, at the beginning of that scene Cullen says something and then stops and gives her this longing look, to which the Inquisitor can say "do you ever stop working", "is something wrong" etc, does he do that in all situations regardless of whether you've flirted with him or not?