I don't know much about 5e. I've only read a few things to better understand this game, but from what I've read I'm not sure what kind of entity makes a pact with a hexblade. Something from the Shadowfell?
But is that entity in the weapon of the Hexblade? Is it someone called the Raven Queen?
It's deliberately left a little vague exactly what you're making the pact with, presumably to allow for multiple interpretations even though I find the flavor to be a lot more restrictive than most other warlock options (there are lots of different individual fiends and fey with different goals and themes to choose from, for example, but "shadowy entities/forces that manifest cursed/magical blades or maybe the Raven Queen" doesn't invite a whole lot of diversity in concepts).
If so, how does that fit in with Wyll's story of hunting down the devil he made a pact with?
It has nothing to do with it at all. That being said, you or they could just ignore the flavor behind the Hexblade if you/they don't feel that it fits. For my money, though, I'd expect the official approach to be that Wyll keeps the Fiend patron and gets Pact of the Blade when it's introduced (assuming that Hexblade makes it into the game, though, I'd expect a "Wyll is a Hexblade now"-type mod to crop up pretty quickly).
