Boy is that wikipedia article riddle with citation needed around the part mentioning Joseph.
The thing that points to Joseph being of the Hyksos, looks to be what I thought was the best evidence against it. If you didn't think of this yourself, permit me to state the obvious, The evidence is in where the bones went. Joseph wanted his bones buried where they came from, so unless they, and everyone else, forgot where they came from, they buried him in the wrong place. But if they came from Canaan and went back to Canaan then that's rather appropriate.
However, and with the help of the only reference to Hyksos on Vatican.va translated into English, the key is in the revulsion that the Egyptians felt towards Joseph and his brothers.
Genesis 43:32 (DRA)
32 And when it was set on, for Joseph apart, and for his brethren apart, for the Egyptians also that ate with him, apart, (for it is unlawful for the Egyptians to eat with the Hebrews, and they think such a feast profane:)
If there is evidence of revulsion (or evidence of future subjugation) then yeah, that could be the historical Joseph story. But if there's no evidence for this, then they're separate folks.
Which may be the reason some are hesitant to jump on the Joseph as Hyskos bandwagon.