How is it a problem, though? It doesn't conflict with anything established prior to 'PROMETHEUS'. If anything, the Jockey being an Engineer makes it much more enticing. What was the Jockey doing with that cargo, anyway? Was it intended for Earth? ...maybe for someone else entirely, presumably an enemy Engineer faction?
We know that the Engineers made us. They also made a weapon to destroy us in the form of the black goo... isn't it more than just a little convenient that this race of 'Gods', so intent to destroy us, have a crashed spacecraft sitting on a desolate planet with a cargo hold full of bio weapons that neatly attaches itself to a human face?
Oh yeah. The Jockey being an Engineer is a neat twist on the identity of the derelict's pilot - far more intriguing than it being some goofy elephant nosed 'Star Wars' refugee. lol.
-Windebieste.