It makes no sense to frame an American college student and a prominent Doctor's son.
It. simply. does. not. make. sense.
If the police were trying to protect Rudy, they would most likely frame a less significant person, one unlikely to attract so much attention and possibly one financially incapable of mounting any sort of reasonable defense. They could have kept Patrick even, the Swiss professor's alibi for him had holes and Patrick did some things which could have looked particularly incriminating such as changing his cell phone the very next day.
If they were trying to frame Amanda and Raffaele you can be sure there would still be enough of Meredith's DNA on the knife to retest and confirm the results and there would be plenty of Raffaele's DNA on the bra clasp as well.
What about pangs of conscience? Even hardened criminals suffer these. I don't believe Rudy would continue to allow these two to rot in jail for him.
It requires much more than police misconduct to believe in a framing of Amanda and Raffaele. Most people are aware police misconduct certainly exists but a collusion between all police, prosecuters, judges, forensic scientists and more is a whole other ball game.
Do you honestly think Perugian officials would wage an elaborate campaign to frame two innocent, high-profile people, one an American for which there was certain to be international involvement and backlash, the other a prominent and wealthy Doctor's son, to protect someone like Rudy Guede? Even if he had an inside track to the drug scene, I doubt they would feel the tradeoff was worth it. Rudy was expendable.