I think Kubrick would have cut the ending
Yes I know that it was all his idea so don't attack me about that.
However there are two things that make me think he probably would not have included it in the final cut.
1. Kubrick preferred ambiguous endings.
Nearly every single film of his has an open ended conclusion that is up for interpretation. He always wanted people to think about his movies and come to their own conclusion. The ending to A.I spells everything out quite plainly (in the worst possible disney fashion) and really the only interpretations that have been made are about finding religion, which isn't very thought provoking when considering the story. I think when push came to shove, Stanley would have scrapped his ending.
2. He had already changed endings for his films last minute.
2001 originally had a voice over during the starchild scene that summed everything up and clearly explained to the audience what the movie was about and what was going to happen. Although Kubrick penned this ending, he realized it wouldn't work and cut it.
The shining originally had a scene where we visit Danny in the hospital, they talk about how they couldn't find jacks body and Danny is given the tennis ball from earlier in the movie. This was actually in the final cut until Kubrick requested that theaters cut the scene out of the film reel and send them back to the studio. They were then destroyed. While this is still an ambiguous ending, its more convoluted than the ending we have and Kubrick had the good sense to remove it, instead relying on a haunting visual to engage the audience.
The last chapter in a clockwork orange was not included in the film. This featured Alex realizing he needs to change his ways and get married. Now it is known that Stanley first read an American copy of the book which also omitted the last chapter, so it is often just seen as something he didn't know about.
However, it seems unlikely that he wouldn't find out about the original ending from anyone while making the movie, which was filmed in the UK and had an all british cast. There is no way that not one actor or producer (or the damn author) who read a british copy of the book would not ask about the missing ending or even bring it up. He had to have found out at some point and made a conscious decision to still not include it.
Point is, the man knew when to change his ideas. We also need to keep in mind that Kubrick always wanted Steven to direct it, so this scene (and the whole movie) was written for Speilberg's straightforward hollywood style, not Kubrick's style. Stanley worked on this film for years and when he finally did accept that he would direct it, he died shortly after. We have no way of knowing what changes or alterations would have taken place, but I am damn sure that he would not put that ending in his version of the film.
You can try and rationalize that the scene would still be there all you want, but the fact is that it is a horrible sequence, and Stanley would have realized this.