The poisoned apple scene has been contested by his grandson, but there are others who claim it happened (including Oppenheimer himself) so the assertion that it didn't certainly isn't established fact. Also, the scene works well dramatically in the context of the film.

I think the scenes with Pugh were good, personally. They had a Doctor Zhivago-ish passion to them and I think the film did a good job of conveying her enigmatic character, as a committed communist, and as a socially unconventional, sexually liberated woman, who was nonetheless troubled. She doesn't come off as a femme fatale in my opinion.

Perhaps this is down to personality and temperament, and I can only speak for myself, but I definitely felt the impact of her death, and I think Oppenheimer did care, in terms of how he is depicted onscreen. Indeed, he is distraught and haunted by her afterwards.