Hardly.
I guess one can argue that fleeing from Obito with Naruto was cowardly, but he couldn't exactly fight at his full potential with a baby in one hand. I'd say that case is justifiable.
I don't recall Minato fleeing from any other fights after that. Sure, he lets his opponents go after they've been outmatched, but that's just his character. He is not a ruthless killer and followed Jiraiya's ideas of peace. Killing Ay or Bee would only have made Kumogakure hate the Leaf even more, which could have easily escalated into a situation where the war between them would still be ongoing.
As for Obito, there wasn't much else Minato could do. His priority was to finish the battle as soon as possible to deal with the Kyuubi; there was no point trying to pursue Obito further if it meant the village would suffer more destruction.
If they had clashed again after that point, I'm certain Minato would have attempted to kill him rather than simply deter his motives.