The title says it all, really. I suppose that it could be reversed to be that Missingno is really Discord, but while this second idea would probably still be interesting if done well, the first way personally seems a bit more interesting to me.
Anyway, Missingno somehow appears in Equestria generations ago, its very presence glitching the world around it. Its form begins to shift (if it doesn't completely shift on entry to this new world) to that of a draconequus as it learns to somewhat direct the glitching in a way that it sees fit. Meanwhile, the ponies and other races of the world, not knowing what Missingno is, incorrectly assume that it is a spirit, and that this particular spirit is aligned with chaos. Missingno hadn't truly known any languages in its old world, and it is the same here in Equestria, but in both worlds, bits and pieces of understanding sometimes floated through its mind, and from this, Missingno is eventually able to piece together enough to form a very rudimentary understanding of the Equestrian language. It learns of what the ponies had believed it to be for years (possibly for generations), and from that, Missingno begins to build an identity and personality for itself (it may have been unsure of what it itself was).

I suppose that someone may be able to turn the idea into something other than an origin story.