I think Balder likely is not going to exist in the MCU. True, he was in an early draft of the Thor1 script. But there wasn't enough room to deal with his story, so they cut him. And now it's kind of too late (unless they make him just some random unrelated Asgardian, as Jon suggests above. But if they're going to do that, why bother calling him Balder? Why not, for example, "Kemper"
Scholars think that Baldr was added to the myths when Scandinavia was Christianized, so Marvel could explain the reference to Balder in the book along those lines.
They actually could explain away any of a number of elements from myth that they don't want to use in Marvel continuities in a similar manner. Someone makes up something, and before you know it, it's taken on a life of its own. (enough to populate the entire snopes.com website).
A couple of examples: the idea that Vikings had horns in their helmets. Didn't happen. But it appears commonly enough in culture that it has its own entry on the TV Tropes website.
Here's another one: Davy Crockett was a real person. But that doesn't mean he killed him a bear when he was only three. (song reference for those who don't know)
So just because a Midgardian myth says the Norse gods did this or that doesn't mean that the corresponding Marvel Asgardians must have also. They could just say that it was a tall tale that grew up on Midgard around the legend of the Asgardian figure.
Now, the issue of the timing of Thor and Loki being born around 965 CE and having their adventures after that time is a bit more problematic. There is record of Tor/Donar/Thunor/Thunaer/etc. from the 1st, 7th, 8th, and 9th centuries CE. So at best we can say the mythical figure predates the Asgardian and was conflated with the Asgardian (and that, btw, kind of would imply that the Asgardian was named after the Midgardian mythical figure, or that both were named after some third figure that predates them both). But I think it's just an "oops" on the part of the writers, and we'll make a bigger hash of it trying to make it all fit together than to just chalk it up to an "oops".