I totally agree that the 'Heart of Darkness'-like version of INS would most likely have been far better. Some of it remains in INS like the moral dilemma talk between Picard and Dougherty but it is overwritten, Dougherty is simply the bad guy.
That's why the movie is unsatisfying, even if you don't know the background stuff about the first story draft you feel that there was a change of directions during writing, that they couldn't decide whether they wanna make a dark or bright movie.
I certainly would not argue so one-sided if the movie had gone down this more radical road. But it hasn't and has actually become a simple morality tale.