As far as i'm concerned, there is nothing wrong wih Hulk getting his head completely kicked in by a very powerful skyfather, in a 1 on 1 tear up. But it was obvious the Zeus did something, probably after the beating, to reduce his HF-this would be to teach Hulk a lesson about messing with the gods. By the time Hulk awoke to find himself chained up, his HF should've totally healed him up-going by previous examples-so enabling him to be strong enough to break his chains. She-Hulk ripped the chains, with no significant effort, to free Hulk-so even if he was only at, say, 50% he should be able to free himself.
As for possibility, that the beating itself overtaxed Hulk's HF-I'm sorry but that dog don't hunt. The actual injuries the Hulk sustained in the Zeus fight amounted to broken ribs, collapsed lungs and concussion-his HF has taken care of similar and worse damage with no problem. In WWH he had holes punched through him by Zom/Strange and kept fighting. Professor Hulk was stripped down to a nearly a skeleton by Vector of the U Foes and he recovered in seconds-no overtaxing there. Maestro used a gun, designed to kill him, to blast several holes through Professor Hulk and then delivered a vicious beating with his fists-as Maestro was twice a strong as his younger self this was similar, though not as severe as the Zeus beating. He tricked Maestro into a time machine before Maestro could finish him and then a few minutes later was nearly fully healed.
As I said before, Zeus real punishment wasn't the beating itself, but what came after.
Back to topic though, Zeus hands DD his head