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Most universities do not eliminate your lower grade from your GPA calculation, some might but thats going to just artificially inflate your GPA.
I know that at my undergrad college, they had this thing called the "freshman forgiveness" rule. Basically, during your freshman year you were allowed to fail a certain number of credit hours (I think it was equivalent to 2 or 3 classes) and then retake those classes. Only the second grade would be factored into your GPA, but the original grade would still remain on your transcript.
Personally, I would use the GPA that appears on your official transcript. Even if the schools you're applying to question the appearance of that D+ on your transcript, I think that they'd be hard-pressed to argue with you self-reporting what the school says is your official GPA.
Or, I would just call the schools to see what their policy on this sort of thing would be.