Why would they want to screw over a dead guy, though? It's not like he's going to be around to be pissed anyway. The fact that Eli HAS been indirectly mentioned in the comics and we HAVE seen his image being used in flashbacks and a variant cover seems to indicate Marvel still wants him as a part of their universe. I think if their goal was to erase Morales's work and its legacy from existence, they wouldn't even be acknowledging that they exist.