I had the same reaction. It was an unwise remark, and may even have revealed some wishful thinking on her part, but I agree with your interpretation. That said, I wouldn't mind if her political career died a permanent death as a result!
Obama is the first black candidate for the Presidency from a major political party. Don't forget, Obama was the first candidate in history to receive Secret Service protection during the early primaries (other than the former first lady) due to perceived threats against him.
This was a serious "gaffe" by Mrs. Clinton. With one sentence she paints herself as the Manchurian candidate and insults the Kennedy's on a most personal level.
She may be able to spin it, but she'll not erase it.