Well for starters, I'm not sure where you have that impression. By 1860, Francophones were a minority population in Louisiana. Based on what information I can find on this, they made up roughly 30 percent of the state population, and at least for those in urban areas, bilingualism was hardly uncommon, as English was the language of business, so creole merchants would need to have at least conversational fluency (this in comparison to the rural Acadians who were generally quite impoverished and less likely to speak English with any appreciable skill).

Now, as for the Francophones in the Confederate Army, certainly some units were composed of ethnic-French, and it is no coincidence that Zouaves-styled units of the Confederate Army hailed disproportionately from Louisiana. In units that were predominantly French, the use of French language for drill was common in those units, even if not all members were French speakers. The French-speaking units weren't always the best in combat, but quite the spectacle on the parade ground, and other Confederate units were impressed by the French-styled show they would put on there. There was eventually a push to change drill over to English, as it was deemed that English language drill would better integrate these units into the overall military structure, but it doesn't seem to have been especially problematic prior, even if it did present minor communication barriers in the day to day. Francophonic officers at least had some command of English - Gen. McLaws described the Colonel of the 10th Louisiana, col. Marigny, as speaking English "indifferently well" - but it was at least sufficient for basic military needs.

Estaville, Lawrence E. "THE LOUISIANA FRENCH LANGUAGE IN THE NINETEENTH CENTURY." Southeastern Geographer* 30, no. 2 (1990): 107-20.

Jones, Terry L. Lee's Tigers: The Louisiana Infantry in the Army of Northern Virginia

Seymour, William J. The Civil War Memoirs of Captain William J. Seymour: Reminiscences of a Louisiana Tiger