Fr. Weninger continued his missions during the Civil War, but his memoirs reflected a growing resentment for its causes and progression. The political scenes in the North caused concern for Weninger who saw impending difficulties for Catholics who served with the Union Army. Catholic clergy from Northern states put forth their grievances and perspectives on the war. They pointed to slavery as the primary evil and root cause for the war and their concerns varied on the political spectrum. Weninger adopted a unique position in criticizing all factions and stressed uniform reconciliation. Even though Weninger did not identify himself as Republican or a Lincoln supporter, he was convinced slavery was the greater evil:

‘…Weninger was convinced that the north was in the right. He blushed on account of the company he was in because of that statement but he consoled himself with the reflection that just because a person agrees with the north does not make him a member of the republican party.’ (Benjamin Blied, Catholics and the Civil War 129).

Weninger believed slavery created radicals within the South who instigated the secession. He argued that rebellion was unjustified and criticized politicians for mishandling the crisis. The rapid influx of Irish Catholic immigrants that were quickly conscripted for the Union army disheartened Weninger for both religious and political reasons. Factions who despised Catholics and paid substitutions benefiting the wealthy who could avoid military service put an enormous stress on Weninger seeing many of his fellow Catholics die. Many still enlisted for the chance to prove themselves as Americans and to remove many of the instilled prejudices that had branded them as un-American though (Sean Fabun, “Catholic Chaplains in the Civil War,” Catholic Historical Review, 99 no. 4, 675). As those Catholics enlisted and fought for the cause, Weninger further criticized the Republican Party for its anti-Catholic influence of ’48 Germans (those who participated in the 1848 Revolutions and resented Catholicism) and residual members of the Know-Nothing Party.

(Regiments like the Irish Brigades of New York were predominantly Catholic and often held Mass before battles)

‘Of course, all Republicans were not so better; but many, and those most influential, were, and hence the danger which hung over the Church. Even whilst loyal and brave sons of that Church entered the army and shed their blood for the cause, dark threats resounded over the land.’ (Francis X. Weninger Papers, Jesuit Archives-Central United States, 209).

Staunchly against Democrats and their support of slavery and Republicans for harboring anti-Catholic dissidents, Weninger resigned himself from directly participating in the political or military conflict. He understood the military actions, but what concerned him was the situation of slavery following the war’s outcome:
‘The North now has gained victory and after victory, and it seems that the war will not be of long duration, but that does not mean that things will be happily settled. The great question of slavery remains, the issue of which cannot be foretold…If slavery continue, the root of the evil will remain, and sooner or later there will be repetition or all the trouble and discord, for so bitter is each [political] party, and so violently are their passions aroused, that a reconstruction of the former status quo is not to be thought of…the fitness of the negro for any species of labor can never be sufficient grounds for the perpetuity of slavery.’ (Francis X. Weninger Papers, Jesuit Archives-Central United States, 209).

These concerns were a combination of the well-being of liberated slaves and the public reception of the Catholic Church. Proposals such as slave compensation for owners and African re-settlement did nothing for the well-being of blacks themselves as Weninger believed and he overrode these with the idea of national emancipation and atonement:

‘Should the abolitionists gain their point and slavery cease, should the Union be consolidated upon a new and permanent basis…doubtless there will be grievous trials in store for the Church, but at present she has no reason to fear. Divine Providence in this present juncture watches over her.’ (Francis X. Weninger Papers, Jesuit Archives-Central United States, 240)

Weninger assuaged the moral issue over slavery by arguing the need for avoiding the political backlash and simply carry out emancipation and reconstruction through faithful devotion. He acknowledges the political factor within Church operations and what he saw precipitated the oncoming issue of black evangelization in a post-Civil War country. Slavery had established a version of the U.S. when Weninger arrived, but now he saw the Church as a catalyst in creating opportunities for newly liberated peoples to lead religious lives out from underneath bondage. He knew that freed slaves would face a mountain of obstacles, but within those challenges were golden opportunities for spiritual awakenings.