According to Rabbeinu Bachaya, Yaakov Avinu objected to the deception that preceded their execution of the male Shechemites, and not the actual execution.
In Bereisheit 34:13, Rabbeinu Bachaye explains:
And the permission [heter] that the sons of Yaakov, Shimon and Levi, found to spill innocent blood was written by the Rambam of blessed memory because bnei Noach are commanded in the 7 mitzvot and the laws included within them, and a ben Noach that transgressed and stole or abducted or violated the daughter of his friend or enticed [pitah] her is condemned to death by sword [b'sayif].
And so, he who sees one that transgresses one of them [the 7 mitzvot] and they didn’t bring him to justice to execute him, behold, the one who sees shall execute him by sword [b’sayif].
And because of this, all the men of Shechem were guilty because, behold, Shechem [the prince] abducted and violated and they saw him and they knew and didn’t bring him to justice.
But the exemption [heter] that Shimon and Levi found is clarified because the people of Shechem were wicked, worshiped idols, steeped in licentious behavior [megalei arayot], and like the matter that is written of them (Vayikra 18:27): “For the people of the land who preceded you did all these abominations and the land was defiled.”
And they executed the prince and all the men of the city because everyone supported his path…
I’m guessing it’s the death penalty because all forms of stealing (which also include abduction and the violation of women) receive the death penalty for bnei Noach.
And because pitui is an aspect of geneivat hadaat—“stealing of the mind,” meaning to deceive and give the wrong impression, then it’s a form of stealing.
But I don’t know for sure; that’s just the only thing I can figure.
Interestingly, Rabbeinu Bachaye lived in Muslim Spain 1255-1340.
How did he arrive at such a "radical" female-sympathetic idea in such a chauvinistic culture 7 centuries ago? His sympathetic attitude certainly could not have been an influence from his surrounding culture or time.
In fact, his surrounding culture would've thought Rabbeinu Bachaye downright wrong, weak, or crazy for believing such a thing.
(Remember: This culture still kills girls in this kind of situation, even if they're very young and even if the criminal nature of the crime is very brutal and obvious.)
I guess it must just be from the Torah itself.