Yes Captain Marvel has the strength of Hercules/Heracles, but he isn't relegated to the Marvel Universe. Both DC and Marvel use the various Greco-Roman and Norse gods in their storytelling. So, Superman beating Thor in the JLA/Avengers cross-over and Thor having once beat Hercules doesn't mean Superman could beat Captain Marvel. Because writers from both companies tend to illustrate characters with various levels of power it isn't easy to make this conclusion. Plus I think there is great contention as to whether Superman could actually defeat Thor. There are many Marvel fans who think Superman got lucky.
In the traditional, meaning non-comic myths surrounding Hercules, he was killed by being burned on a pyre of oak by his friends. He had been mistakenly poisoned by his wife Deianira, and asked to be burned because it was less painful. In Homer's Iliad, Odysseus sees Heracles in Hades, although there is much consternation as to whether or not the passage is original to the epic;
And next I caught a glimpse of powerful Heracles—
His ghost I mean: the man himself delights
in the grand feasts of the deathless gods on high...
Around him cries of the dead rang out like cries of birds
scattering left and right in horror as on he came like night...
If you want to read the entire passage, it is found in the Odyssey episode XI or the Nekuia. This passage indicates that the "ghost" of Heracles resides in Hades but the "man himself" lives on Olympus. This is probably as result of conflicting depictions of the character and trying to appease both sides.
The Roman myths, where he is called Hercules, are more definitive when calling him a god, in that the burning of his mortal body upon the pyre allowed him to become a god and live with the other Olympian gods. However the Romans adopted these stories from the Greeks and altered the tales to suit their needs. The point of all this is, if you take the original Greek myths, and place that character into the Marvel universe then Thor beating a mortal man is no big deal. It doesn't prove that Superman is stronger than Captain Marvel.
Thanks for the insight! I guess we will never know the answer.