Page 28 of the rulebook:
"A creature may make one counterstrike against each creature that attacks it with a melee attack (even if the attacker attacks it with more than one strike during the attack). Multiple Counterstrike traits on the same creature do not allow it to make additional counterstrikes."
This line is a little vague. It could be interpreted as one counterstrike per attacker per attack, allowing you to counterstrike the battle fury. Technically additional strikes are additional attacks though, so this interpretation would lean itself to allowing you to counterstrike those as well, but we can clearly see in the example that such is not allowed. Therefore I think the correct interpretation is one counterstrike per attacker per attack action. There is room for disagreement, you may feel that the exclusion of additional strikes is a specific ruling rather than just an example, but I feel fairly confident that per attack action is correct.
So I'd say no, you can not counterstrike a second time with the Hydra.