Hm. Well I certainly don't think you "missed the chance" (I don't think this can happen). But when I decided to kill him, I had a conversation with him (there's dialogue where you tell him the Blades want him dead, and he says they're right to not trust him) but afterwards he continued to just sit there on his little dragon couch wall thing. I fired one arrow into him, health dropped, he doesn't react. Two arrows, same thing. On the third arrow he finally became aggro and started flying. Dragonrended and he died like any other dragon.
Perhaps it's a little glitchy.
I found that attacking him after the MQ wa over had no effect. He never took off, just sat there and took it until his health went down to zero, and still didn't die. I didn't think to try Dragonrend on him because he never flew. I tried multiple reloads, but always got that result. When I tried it as soon as you got the order to kill him, the first attack went the same way. I reloaded and tried, and this time he took off and Dragonrend etc worked, so I killed him. There seems to be a bug, and if he doesn't take off, he's not killable.