As far as I have been able to ascertain, there was growing antisemitism in the United States during the Civil War, and in the Union Grant had even expelled Jews from sections of his staff, but I wasn't able to get any sources regarding the confederacy.
I'm looking into this for a character in a tabletop game, and realized there was a severe lack of sources for this. Any help is appreciated.
Grant had even expelled Jews from sections of his staff
I don't know of grant expelling Jews from his staff. He did expel Jews from Kentucky, which was reversed quickly.
Anyway, prior to Eastern European Jewish immigration the south had significant Jewish centers, until they were overshadowed by the Northeast. Besides the already-mentioned Judah Benjamin in the CSA cabinet, a Jewish guy was Quartermaster General. A number of Jews served in the Confederate Army, too--there were significant communities in several cities, particularly Charleston. There are also a number of Jewish memorials to Confederate troops to the south.
So while there was discrimination to an extent (as was the case everywhere in the 19th century), Jews were not excluded from the government wholesale.
Generally speaking, the Confederate South was uncharacteristically tolerant (that is, relatively tolerant, to clarify) of Jews. Some 2,000 Jews actively and proudly fought in the Confederate ranks (mostly immigrants, not primarily from the long-standing Jewish-American families, although they too certainly contributed) and Jews also served in prominent political positions. /u/gingerkid1234 explained this well.
However, this being said, it should not be ignored that there certainly was an outpouring of anti-Semitism as Southerners looked to leave the responsibility for their hardships on scapegoats. Many of the Confederate ills were in fact blamed on prominent Jews in the Confederate government. Both Judah P. Benjamin's and Abraham Myers's motives and actions were often questioned and suspected precisely because they were Jewish. In one instance, General John Winder swore that:
all the distresses of the people were owing to a Nero-like despotism, originating in the brain of Benjamin, the Jew.
In another instance, a Confederate war clerk remarked that Benjamin was not merely corrupt in his own self-interest but that he was partly responsible for the alleged plundering of the country by Jews, more generally—that the Jews in the South did more harm than Federal armies:
An immense sum is to be sent West to pay for stores, etc., and Mr. Benjamin recommends the financial agent to the department. The illicit trade with the United States has depleted the country of gold, and placed us at the feet of the Jew extortioners. It still goes on. Mr. Seddon has granted passports to two agents of a Mr. Baumgartien—and how many others I know not. These Jews have the adroitness to carry their points. They have injured the cause more than the armies of Lincoln. Well, if we gain our independence, instead of being the vassals of the Yankees, we shall find all our wealth in the hands of the Jews.
Myers too was accused for helping fellow Jews at the expense of the common good:
the people feed and clothe the armies in spite of the shortcomings of dishonest commissaries and quartermasters. They are now sending ten thousand pairs of shoes to Lee’s army in opposition to the will of the Jew Myers, Quartermaster-General, who says everything must be contracted and paid for by his agents, according to red-tape rule and regulation....[Also, t]he late Secretary of War, Mr. Randolph, has formed a partnership with...Myers. To-day a paper was sent in by them to the new Secretary, containing the names of ten clients, all Jews and extortioners, who, it appears, at the beginning of the war, and before Virginia had fully seceded, joined several Virginia companies of artillery, but did not drill with them. They hired substitutes for a small sum, all, as the memorial sets forth, being foreigners of the class subsequently exempted by act of Congress. And these counselors demand the exemption of the Jew extortioners on the ground that they once furnished substitutes, now out of the service!
The same clerk also wrote angrily to his diary, expressing feelings all too common throughout the South, that:
The Jews are at work. Having no nationality, all wars are harvests for them. It has been so from the day of their dispersion. Now they are scouring the country in all directions, buying all the goods they can find in the distant cities, and even from the country stores. These they will keep, until the process of consumption shall raise a greedy demand for all descriptions of merchandise...
...Still the Jews are going out of the country and returning at pleasure. They deplete the Confederacy of coin, and sell their goods at 500 per cent. profit. They pay no duty; and Mr. Memminger has lost hundreds of thousands of dollars in this way...
...[W]e are in danger of being sold to the enemy by the blockade-runners in this city. High officers, civil and military, are said, perhaps maliciously, to be engaged in the unlawful trade hitherto carried on by the Jews.
In a more objective observation, he noted that:
A Jew store, in Main Street, was robbed of $8000 worth of goods on Saturday night....This is significant. The prejudice is very strong against the extortionists, and I apprehend there will be many scenes of violence this winter.
In the Confederate Congress, numerous Congressmen also expressed their opinion that the Jews were to blame for much of the misfortune facing the Confederacy. Henry Foote put it thusly:
It was notorious that our land has been recently deluged with foreign Jews....At least nine-tenths of those engaged in trade were foreign Jews, spirited here by extraordinary and mysterious means...[They are] permitted in many cases to conduct illicit traffic with the enemy...[I]f the present state of things were to continue, the end of the war would probabbly find nearly all the property of the Confederacy in the hands of Jewish shylocks.
Foote believed that it followed naturally and immediately that the proper remedy was to prohibit Jewish immigration entirely. Other congressmen agreed, and offered their own observations to the same effect. For instance, Robert Hilton said that the Jews
swarmed here as the locusts of Egypt. They ate up the substance of the country, they exhausted its supplies, they monopolized its trade. They should be dragged into military services.
While certainly harsh, Confederate attitudes were broadly, as I said, actually relatively tolerant (it must be remembered that the Confederate Congress never passed the measures proposed and urged by such men as Foote and his colleagues). However, despite some amount of ill-will, lots of talk, and a few violent outlashes, Jewish Confederates found themselves facing far less intolerance and violence than they might elsewhere in the world at the time. Most Jews who fought in the Confederate ranks were proud of their service and most Jews were completely loyal to the Confederacy and their fellow Confederates. Indeed, southern Jewish communities sent a larger proportion of their populations to fight than did the general population.
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