I don't agree with the comments that claim the film glorifies or enjoys the act of rape. In fact, by choosing one, and the main, character (Noodles) as the rapist in both cases, the film makes it easier for the audience to relate the violent sexual behavior with Noodles's past experiences and resulting incompetence in communicating with women.
Far from coming out victorious from these acts, he can never make up for them. Even in the first case when the gang get the tip for robbing the jeweler from the rape victim, Carol, and it is shown as "making it look real", Carol afterwards complains about the painful aftermath of the violent act, chooses Max rather than Noodles, and their relationship never heals.
The second time, when he rapes Deborah, Noodles loses the woman he is obsessed with forever. Even the chauffeur who drives the car where Noodles rapes Deborah, regardless of Noodles's power, money or reputation, clearly expresses his disgust in what he witnesses. This clear instance of rape is shown in its relation to Noodles's obsession and as a cause for irreparable collapse of his relationship with a woman who knew him and his past experiences very well. Moreover, Deborah, like Carol before, chooses Max afterwards.
Although the film does not seem to favour any particular way of life, friendship or relationship, it appears to make a statement about its stance around the act of rape.