He knows everything Rick has going, and he called himself Negan almost immediately after entering The Sanctuary.
All the proper Negan would have to do is threaten to pinch him with tweezers, and Eugene would squeal his darkest secrets.
And who has better opportunity and motivation than Eugene at this point?
But now that he’s shown his true colors — which are just various shades of yellow — it’s almost hard to believe that he’ll do something to help the protagonists later on.