Just to play devils advocate here... Tarantino has a very informal approach to interviews and so i could possibly interpret this passage slightly differently:
"...and you know he kills the girl at the end, I would have had him kill Vespa at the end "
Could QT actually be saying that he would have chosen to have Bond kill Vesper at the end? As in:
"...and, you know, he kills the girl at the end."
To clarify - it could be a Tarantino conversational way of saying "...and, you know [what i would do differently], he kills the girl at the end."
It may seem a stretch, but having watched my fair share of QT interviews over the years, i've often seen him abbreviate in this manner. Either way, whatever one thinks of his movies it's surely hard to disagree that his scripts are particularly exceptional. A man that writes so well, winning Oscars for his scripts, surely needs to be given some benefit of the doubt when it comes to his comprehension of the written word. So i'm going with my theory that he didn't misinterpret Fleming's ending (or forget), but intended to adapt it
Perhaps he'd have a point - in this day and age would the intended harshness of that final line seem as harsh - perhaps QT felt that to get Fleming's point across - of Bond's transformation from idealist to realist - his end of innocence and the beginning of his bloodlust - to a modern highly desensitised audience the point has to be underlined by being the action of Bond killing Vesper, rather than just the words alone. That would be turning words into actions which is exactly what good cinema, such as The Artist (2011), or Mad Max: Fury Road is about, after all.
For the record, personally i prefer Vesper's suicide; if Bond kills Vesper, then the final 'The bitch is dead' line loses it's shock value and becomes redundant. It would play as deadpan, more befitting Philip Marlowe than Casino Royale's James Bond. But i can see the cinematic-grammatical logic to QT's alternative.
As for his notion to end the movie with the book's final line! Well i've bored you all far too many times already with my opinion that as nice as the 'Bond, James Bond' ending of Eon's CR was, i would've preferred to see it end Fleming's way, rather than throwing the line away as they did. It seemed as though Eon were afraid that the line's intentional harshness would alienate the audience, but were also afraid that to leave it out altogether might alienate (some of) the fans. So it's fudged midway into an expositional conversation - barely noticeable... So IMO kudos to QT for recognising the importance and power of Bond murdering Vesper's memory with Fleming's closing line of CR.