I'm not sure where to even start on this. Inbreeding does not guarantee cross beaks or any other genetic defect. Inbreeding reduces genetic diversity and can enhance certain traits. Some of these traits may be good and some may be bad. It's quite possible you will get some of both. Chickens have a lot of different traits.
There are techniques breeders use to help maintain genetic diversity. These usually involve either a lot of chickens (pen breeding method, for example), or separate breeding flocks and really good record keeping (like Spiral Breeding). Most casual backyard flock owners can't really do either so it is best to occasionally bring in new blood. A very important part orf this is to carefully choose your breeders, male and female. Hatch eggs and choose your breeders from adults that have the traits you want, whether those are physical traits or behavioral traits.
There are studies that show that inbreeding can reduce fertility, especially with the roosters. "Can" does not mean that it absolutely will each and every time, but that it might happen. Studies have shown that it might happen and it is usually associated with the rooster when it does happen. But the studies I've seen involve fertility, not rape. Do you have a reference or link to the study about behavior? I'd be interested in reading it.
Some people consider any chicken mating to be brutal and vicious. I don't. It is an instinct-driven process where the roosteer and hen both need to work together. I hold the hen as respondible as the rooster to do her part correctly. Some roosters are brutes and need to be removed from the flock.
Adolescence can be a rough time on roosters and hens. By that I include adolescent hens as well as adolescent roosters. Maturity usually solves those problems. If I see a problem with only one hen in the flock and they have matured, I remove the hen and the problem goes away. When that solution works, I consider the rooster not to be the problem because that problem is not associated with any other hens.
I'm not aware of any breeds where the roosters are specifically gentle with the hens. To me, it depends on the personality of the individual rooster and the individual hen. Maturity of both plays a big part. If you breed roosters that are gentle with the hens, you are more likely to get a rooster that is gentle with the hens. A big part of that "gentle" is because the rooster has the traits and personality that he can dominate the hen, she accepts his dominance, and will do her part in the mating ritual.