Okay so I'm having to answer my own question on the same day I posted it so that this question doesn't get closed as off-topic "opinion-based". I don't like having to do this but I feel I have a solid question here.
According to jamescamerononline.com "We've got a story worked out but it hasn't gone beyond the talk stage" - James Cameron on Terminator 2 in English Magazine 1985
William Wisher: Jim pulled out this old yellow sheet of paper from a notebook and handed it to me without saying anything. there was one sentence scribbled on the dog eared page. It read: Young John Connor and the terminator that comes back to befriend him. (The Making of T2, 1991)
This shows that Cameron's original logline spoils the movie right there.
However the article that OP (That'sa me) linked doesn't pull this "the marketing spoiled the idea of who's the bad terminator" out of nowhere it directly states it on the jamescamerononline.com that "The movie is designed in such way that the audience doesn't know which of the time travelers is the good guy. The way the movie is shot and the story and angles constructed is to make them think that T-800 is the antagonist and T-1000 a human character. T-1000 is never shown to kill the cop or copy his clothes and seems very genuine when talking to John Connor's foster parents, while the T-800 is shown to go through the bar like a tank, crushing hands, breaking arms and seriously injuring people."
So did James Cameron spoil his own script that he wrote? He had complete control of the movie for almost all aspects it seems strange that marketing got away from him. I haven't found a direct quote referencing this but there is this quote from the same website "James Cameron (Globalnet): On T2, I wondered if I could get the audience to an emotional place where they would cry for the Terminator. That was my goal: Could I take world's coldest motherfucker and turn you around in a two-hour time period to where you actually felt sorry for him? Forget about all the hoo-ha with the liquid metal guy: that was fun, but getting the audience to cry for the Terminator was the big cinematic challenge. That's the reason I made the movie"
So yes there was an intentional story development of suspense as to who the evil terminator was supposed to be. Marketing definitely blew a hole in this by stating point blank who was good and who was bad. However it did not spoil anything. The suspense is meant for the story itself and even knowing what the marketing of the movie was before watching there are two things that would keep the suspense going despite knowing who is good and who is bad. One marketing is wrong a lot and sometimes misleading on purpose. Two the T-800 is so ruthless it seems like is still the bad one even after the reveal. It's not until it saves Sarah Connor that safety is guaranteed with this machine. Plus one more thing from the characters perspective of John and Sarah Connor the T-800 is the bad guy. That is who we watch the movie from the perspective of.
So no it wasn't spoiled and yes most likely Cameron was onboard for this marketing as it didn't change the storyline. His really intention and the payoff for him was to make the audience care about the T-800 as it sacrificed itself.