The simplest answer is that this was the norm, not a departure from it. The US government did not have a complete professional civil service at that time. Every elected politician was in charge of filling some government offices and shifting through a great multitude of patronage requests. If you've seen Lincoln with Daniel Day Lewis, it dramatizes this pretty effectively. The Stalwarts did not devolve into "corrupt patronage" they rose to power in that system. So why then did they wish to keep it?

The Grant Administrations of the 1880s was in some select ways the most socially progressive administration on racial issues that the country would see for a century. Critically however, the society at large did not share this commitment. This was a time where as Republican army officials and black Americans were reporting horrific crimes perpetuated by racist movements, as elected governments were being overthrown by armed white militias, there was a set of press dedicated to painting an entirely false narrative. Some spoke of perfect racial harmony in the South, some painted the victims of terrorism as the perpetrators. Imagine modern disinformation and controversy paired with a complete lack of video footage. That was Reconstruction America. Many white Northerners simply grew tired of the Southern mess over time, they wanted a return to normalcy. The war was over, the economy was going into decline, why should they support all this expensive interventionism?

By the time of the Stalwarts, public support for Reconstruction and Civil Rights was in decline, Reconstruction was in dire peril, and many (including President Grant) felt that the second quieter Civil War for the future of the South was being lost. Those opposed to civil rights had seized on corruption and civil service reform as popular issues with which to tar the Republican party and redeem their own image. Those opposed to civil service reform felt that it risked upending the powers that kept them in office.

Keep in mind the Radical Republicans were at the height of their power when a large part of the country was militarily occupied. While many involved in the war had their own attitudes about race profoundly changed by that experience, seeing first hand the bravery and competence of black Americans, as well as the truth of how they were treated, 1870s and 1880s America was not suddenly free of racism. Punishing Southern traitors might be popular (if controversial), but ensuring that landed gentry had their lands redistributed to the people who actually worked them? Welcoming newly freedmen into the halls of power, into Congress, into the fullness of the franchise? Radical Republicans and later the Stalwarts made a battery of compromises to try and manage the prosecution and aftermath of the Civil War. Patronage was one aspect of the power they held, a weapon to deploy against enemies who came to have public opinion on their side. That didn't mean they were all entirely opposed to reform, Grant pursued a number of anti-corruption measures that seem to have been sincere, even if they were not always effective.

That is not to say that every Stalwart was a saint working with sinful weapons, or that every civil service reform advocate was a racist prosecuting a bad faith wedge issue. The spoils system was a bad way to run a government and there were many good faith critics, including many Stalwart aligned people. Meanwhile many politicians both relied upon it and hated it, feeling that they had to protect it to maintain their power. Modern political fundraising is much the same in this sense.

A couple of last important points of note. One, is that the civil service and patronage is just one aspect of cronyism and nepotism. There are arguments made that the decline of the spoils system and party machine politics increased the amount of power that business interests had over the newly weakened and impoverished political parties. I don't think that fully holds up, but it's important to note that cronyism and nepotism remain in both government and especially in private industry. While it's certainly not as public and dramatic as the large scale change in post office workers occurring every four years, these issues have never gone away. The fact that the Stalwarts are often singled out as being especially corrupt, especially in the context of what came before (and after) them, is really rooted in the successful political strategy of the post Civil War Democrats to end America's experiments in pluralistic, multiracial democracy. Post Stalwart Republicans became ever more reliant on their business ties, becoming the party of business that they style themselves today, as they compromised away civil rights to maintain their grip on the federal government.

What is ironic is that the Democrats' emphasis on the rights of poor farmers, and the end of government corruption, basic principles of fairness, did over time draw to their banner a number of people who became central figures in the fight for Civil Rights.