Good post! I've thought about posting this one myself for quite sometime, but never got around to it for some reason....anyway, I'd have to slightly give it to Thor...
They are both very similar in many ways. Both have near unlimited strength, both have VERY powerful weapons, both weapons have similiar properties and characteristics, both have (or had) a mortal identity, and both are damn near indestructible...
It would be long, brutal, and bloody...but in the end, Thor will be the last one standing. Thor has A LOT more battles under his belt. He's got a ton of more experience, and he's lived a HELL of a lot longer than He-Man has ever seen and experienced...plus, I believe Mjolnir can do a tad more tricks than the Power Sword can!!
Thor was slaying frost giants and rock trolls before Grayskull even stood probably.
Plus, according to the cartoon, He-Man was once hit so hard that he actually reverted back into Prince Adam. That was a ONE time deal and I've never seen that happen to him in the comics, but it did happen. So, I believe a God-Force blast may be enough to KO He-Man and revert him back into Prince Adam....but, this is just my opinion.