I love Pendragon. I love the relatively early start date, and the generational gameplay such a lengthy campaign creates. However, it does create an interesting problem - the rules and genre of the game ask for and incentivize players playing larger than life heroes, people defined by Arthurian ideals of honor and passion and loyalty and courtly grace and noblesse oblige, but then they drop your first characters into the broken world decades prior to Arthur bringing the golden age defined by those ideals. In order to properly contrast Arthur's resplendent, magical, virtuous kingdom with the world before and after, the world before must be filled with the vices, dishonor, and disloyalty Arthur banishes. Yet, with a few exceptions, the rules don't encourage you to have your first character be a bit of a turd compared to his kids and grandkids, to fit the settings they each live within. Instead, you're left trying to live up to the ideals of Arthur's court before Arthur or his court exist to recognize it.
So how do we address that? Well, first of all, even before we get into how the culture and on-the-ground viewpoint of the knights would affect character viewpoints, we can take stock of the situation from an entirely ordinary viewpoint. Obviously if the president raped someone, you wouldn't want him in office anymore, but would you immediately stop paying taxes, or try to assassinate him personally? Probably not. Those especially devoted and diligent in their opposition may spend hours using every available means of litigation and protest and publication to undermine him and try to get him lawfully thrown in jail, but it's considerably rarer that one would go so far as to get themselves imprisoned or executed for the extent of their resistance.
Second, remember that as far as the Great Pendragon Campaign is concerned, the knights really have no way of knowing prior to Uther's death that he raped Igraine. Obviously this doesn't solve the out-of-character issue, but as far as players being more aware of the event timeline than their characters are goes, it's no secret that the guy will immediately thereafter lose two sons, be sick as a dog for years, then get better exactly long enough to watch all his closest friends die around him before he succumbs to the horrible poison as well.
Third, if you're up for a whole lot of creative effort, consider that new stories can result from the characters pursuing more plausible ways to oppose Uther's dastardly activities. If your players really can't countenance serving a guy as he abuses and ultimately kills a loyal vassal before raping his wife, there's a pretty messy yet also wonderfully simple way to resolve that issue - just open up the opportunity for them to swear Homage to Gorlois and serve Cornwall. They can fight to save Gorlois and his castles from Uther's assaults, they can capture the deceitful Prince Madoc who reneged on his honor-bound agreement to help an ally on the continent, they can properly direct their outrage towards the antagonistic King Uther after his magical rape of the duchess comes to light. Maybe they even create a quirky alternate timeline where Uther, rather than Madoc, is the one to perish on the battlefield shortly after conceiving Arthur, creating a brief period where not-very-honorable-but-at-least-opposed-to-rape Madoc takes the throne of Logres and makes reparations to Cornwall in an effort to atone for his father's sins. Things are tense but cautiously optimistic for the next few years as efforts are made to repair relations and Gorlois marries his daughters off to surrounding kings to ally more of the realms against the Saxons. Madoc is, idk, infertile or something, so Arthur stays next in line. (Illegitimate, but so was Madoc, so whatever.) Then bam, all the lords (now including Gorlois and King Madoc) die horribly at a victory feast, Merlin or Ygraine herself run off into hiding with baby Arthur, the PKs play out the Anarchy from a Cornish perspective, and things roughly right course by the time Arthur rises to power, with a few serial numbers filed off and edge cases filled in with new material.