A couple of points:

The song was originally composed in Texas in the 1830s, probably in 1836. However, it remained somewhat obscure until an official version was published in New York in 1858 that became very popular in minstrel shows.

You cannot take the song's original lyrics at face value considering it would have been performed by white actors in black face at minstrel shows, which were essentially productions that lampooned black culture for comedic effect. So considering that the singers would be "darkies," i.e. white men in black face, it would not appear that whites were actually praising the beauty of the mixed-race girl, but rather caricaturing a black man's admiration of her.

Second, troops during the Civil War altered the lyrics in a way that removed an important part of the original meaning. They altered the lyrics from

"There's a yellow rose in Texas, that I am going to see / No other darky knows her, no other darky but me"

to

"There's a yellow rose in Texas, that I am going to see / No other soldier knows her, no other soldier but me."

Similarly, they changed another crucial line from,

"She's the sweetest rose of color, this darky ever knew,"

to

"She's the sweetest little flower, this soldier ever knew."

Thus, the soldiers had removed a level of the original song's praise for the mulatto woman's beauty. The suggestive "rose of color" is changed to the blander "sweetest little flower." Moreover, the original perspective, that of a black man, has been altered to that of a white soldier.

So by the time Confederate soldiers began using it as a marching song, the song's original meaning, i.e. the glorification of a mulatto woman's beauty and her role in the Texas Revolution, had been removed. It became more of a generic tale about a soldier missing a Texas woman, than specifically a black man missing a beautiful mulatto.

Finally, "Confederate leaders" (do you mean like Jeff Davis?) probably did not know or care about the song being used as a marching tune. The strongest evidence for this seems to be that in 1864, Confederate soldiers added in an entire new stanza mocking General John Hood's terrible performance in the Battle of Nashville:

"And now I'm going southward, for my heart is full of woe, I'm going back to Georgia, to see my Uncle Joe. You may talk about your Beauregard, and sing of Bobbie Lee, But the gallant Hood of Texas played hell in Tennessee."

I think if Confederate leaders had actually cared about this song, they would have found the open mockery of a general more incriminating than a vague reference to a mulatto that the soldiers had already essentially sanitized.