The Real Amazons: Hercules wasn't so bad
This inconsistancy is never addressed in the comic when in fact a little closer adherance to the myth on which it is based would resolve the situation quite nicely. In greek myth one of the twelve tasks of Herakles (1) was to get the girdle (2) of Hippolyta (3) for Admeta, the daughter of king Eurystheus. The girdle was a gift from Ares (4) that signified her authority as queen of the Amazons.
When Hercules arrives the Amazons greet him warmly and Hippolyta comes to his ship to greet him. Upon hearing his request, she agrees to let him take the girdle. Hera (5), however, is not pleased that he is getting off so easy. To stop him, Hera disguises herself as an Amazon and runs through the land, crying that Hercules intends to kidnap their queen. The Amazons charge toward the ship to save Hippolyta. Fearing that Hippolyta has betrayed him, Hercules takes the girdle and escapes. Some versions say he slays Hippolyta, but other myths take up her story beyond this point. Either way, it is here that the Wonder Woman version departs from its myth basis, as in no version does Hercules defeat the amazons in battle or enslave them.
But if the encounter with Hercules is based a little more closely on the mythic version he becomes much less of an aggressor, and the conflict between him and the Amazons becomes a tragic misunderstanding set up by mean old Hera. In this situation it makes sense that once he found out, Hercules would feel tremendous guilt for the trouble he had caused the Amazons, and it would be perfectly reasonable for him to bless the baby Diana. A shame the writers of Wonder Woman never researched the myths the story is based on enough to actually make sense of it.
1. the greek name for Hercules.
2. a sort of belt
3. note that the accepted symbolism of taking a woman's belt meant to have sex with her
4. Ares/Mars was the Amazons' patron in myth
5. Hercules' stepmother