I could be wrong, but I just don't see Marvel making Ultimate Nick Fury a bad guy.
First off, they don't want to risk a whole "you made this longstanding heroic character into an African American and then turned him evil...racist" protest.
Second, Avi Arad would give his left nut to make an "Ultimate Nick Fury" movie starring Samuel L. Jackson and making the character evil severely diminishes the likelihood of that film happening.
