No,
First, it is doubtful they would have agreed to take her in. Recall Jonathan's remark to Nancy that "your Dad would love that" -- referring to the idea that Jonathan might live in the Wheeler's basement. He would also love taking in El.
Second, Mr. and Mrs. Wheeler don't know her history - and cannot be told her history. Joyce Byers is now the only adult who knows the truth. It might be awkward to try to explain some things to Mr. and Mrs. Wheeler--- El's tattoo on her wrist, her limited vocabulary and strange behaviors - and what happens if /when her powers start to come back?
Third, if Mr. Wheeler even suspects who El is, he may contact the FBI and turn her in -he still thinks she is a Russian spy.
Fourth, Joyce has a relationship with El already. Note that in the episode "The Bath", Joyce bonds with El when they are preparing her for the bath. In the episode "The Gate", El goes to hug Joyce second after hugging Mike. Joyce is the closest thing to a mother that El has ever known.
So, going with the Byers is the best and only option for El.