I think he was still either in shock that he was air blasted by someone who he thought couldn't bend anything at all, or he was partially knocked out until he woke up in the water and it was already too late.
Personally if I were him I would have water-bent my way out of there rather than confront Korra at all after that. Perhaps found a way to kill Tarrlok before he could spill his story. If people believed Amon dead he would likely have been treated as a martyr, and people would have had only Korra and Mako's word to go on for believing the waterbender accusation. Most equalists wouldn't believe it coming from a pair of benders, and so he could have given it a while and gone underground, not making any overt moves but encouraging the idea that the benders murdered him so they could continue oppressing non-benders.
After he's become something of a legend he returns, rallies folks back to his cause and he's back where he was before in a heartbeat.
Basically, revealing himself as a waterbender instead of pulling a strategic retreat was dumb.
Amon would have had to waterbend away pretty quickly seeing as how he looked like he was running out of air by how heavy he was breathing when he rose up out of the water. And I highly doubt he would have killed his own brother.
I dunno, he did take his bending, and we don't know whether or not Amon himself was capable of reversing that. It's not a huge jump from there to just killing him (Ignoring the fact that it's a Nick show, obviously). And how far would he have had to get to be able to take a breath without being seen? (I haven't watched the finale since it aired so I don't really remember where he was in relation to everyone else.)
Either way no matter what he was thinking at the time he had to know that fighting back with bending would undo everything he'd done until then. Just doesn't really seem like the thing to do while there's still a chance of recovery.
I dunno, he did take his bending, and we don't know whether or not Amon himself was capable of reversing that. It's not a huge jump from there to just killing him (Ignoring the fact that it's a Nick show, obviously).
Amon really believed that bending was truly evil, that it was the cause of all bad things in the world. To him, taking Tarrlok's bending was a favor. He was cleansing his brother of the evil bending. I don't think he would kill his brother, and in his view taking his bending is nowhere close to killing him. He loved his brother.
A couple other cool bits from the panel: Book 2 will bump up Bumi, a fan favorite and brother of Tenzin, to a regular character. His sister Kya will also be a regular. Dubbed a hippie by "Konietzko," Kya's big into healing.