The Imperial view on mutation and deformity in general is based on the way people in medieval Europe viewed them, like a lot of things in 40k.
Being born with deformities is a sign of disfavor from the Emperor, indicating a spirit that is already corrupt at birth, gaining a mutation later in life indicates a truly tainted soul inviting damnation. Penitent mutants who hate themselves for what they are often work to death in factories or subject themselves to horrible public displays of penitence that usually kill them by way of atoning for their corruption. Most Imperial Mutants just scrape a living out of sight of the normal citizens in the worlds where they're common, such as Hive Worlds and Forge Worlds.
In some places any significant mutation is a death sentence, Cadia for example is very strict due to it's proximity to the Eye of Terror, in others it's just a reason to be removed from the roster of citizens and given no legal rights, on Tranch for example they were used as slave labour and ultimately tried to rebel, the mutants native to void ships are also often enslaved by the ship captains to serve as crew in the gun decks.
Abhumans are basically just discriminated against minorities that have to abide by a number of special rules to be allowed to live outside their homeworlds but are otherwise tolerated and possess all the rights of any Imperial citizen. Beastmen are something of an exception since they so closely resemble chaos mutants that most people can't tell the difference. Outside their homeworlds they face the same fates as mutants do despite being entitled to the same protections as Ogryn, Squats and Ratlings.
Amusingly even the forces of Chaos look down on most mutant humans since they cannot provide viable children for creating space marines, making them much more disposable than non-mutated humans to warbands. Doesn't help that most mutants are actually pathetic mewling things rather than terrifying combat beasts.