We don't want to push you to read The Kite Runner as an allegory. Please don't picture us on a street corner, whispering to passersby, "C'mon, try reading this as an allegory. You'll feel really good." That said, Hosseini does explicitly say The Kite Runner is allegorical (source).
In fact, Hosseini specifically identifies the rape passage as allegorical. In the book, however, he painstakingly describes the rape in the alleyway. It's hard not to see exactly what happens in the alleyway in very vivid detail. This makes allegory problematic. Sure, Hosseini does tell us that this scene is allegorical, but doesn't allegory seem more like a barebones outline than the complete essay? Isn't there some point where allegory, if enough details and realism are added, becomes image? A point where the scene becomes so realistic it's hard to remember it stands for something else? All this is to say you can probably read the alleyway passage as either allegory or image. We're unsure ourselves how to read it. On the one hand, Hosseini says it's allegory. On the other, it has the realism of an image. You decide – though in the end, it's probably more palatable if you read it as allegory.
You may ask: How would I read The Kite Runner as an allegory? Well, in the chapters leading up to Hassan's rape, the Soviet Union invades Afghanistan. This means, in the allegorical scheme, Amir would represent the international community who stood by while the Soviets "raped" Afghanistan. We think this reading makes (some) sense. Don't forget Amir later becomes a US citizen – it's not too far a leap to say he represents the Western community.
Let's take it a step further: Just like the international community failed to protect Afghanistan, Amir also fails to protect Hassan. In addition, Assef, the perpetrator, isn't 100% Afghan. His mother is actually German. We understand it would make the allegory really tidy if Assef's mother were a Soviet. However, it should be enough for you allegory freaks out there that Assef descends from a foreign country which is linked to totalitarian rule.
To sum up: it's possible to read The Kite Runner as an allegory, but it's not necessary to your enjoyment of the book. The themes of warfare, violence, and abandonment are so present most readers will connect the story to international politics without saying to themselves, "Amir must represent the international community." Really, the allegory or no allegory question is a nine-iron or chipping wedge conundrum. Meaning, stop thinking about it because either club will get you on the green.