Was that definately Scarecrow at the beginning? Also, wasn't the guy that Dent was torturing Scarecrow? I wasn't positive, especially since he left the first Scarecrow with the mock-Batmen, and while the second one looked very similar, he should have been in jail already (twice!).
Yes, that was Scarecrow. It was even Cillian Murphy when Batman unmasked him. And no, that was Thomas Swift, one of Joker's goons (which Batman says specifically when he finds Dent questioning him).
And at the end of Batman Begins The Scarecrow was missing. He was not taken into custody. Even Gordon mentions that they hadn't found "Crane or half the inmates at Arkham that he freed". So Batman capturing The Scarecrow was actually completing an arc that was established in Batman Begins.