Tell me - one of the Southern Democrats who opposed civil rights? That's not exactly someone I consider to be worthy of an aircraft carrier that represents freedom to the oppressed around the globe.
At first, yes; it was a sign of the times in 60's MS. He wasn't as racist as James O. Eastland, the other Senator from MS with whom he served. Nor was he the blowhard racist that Theodore G. Bilbo had been. Stennis ran for Bilbo's seat, after Bilbo's death.
By the 80's he'd become a strong supporter of civil rights. He's called the "Father of the Modern Navy" because of his support for updating the fleet. I'm sure that's why the Navy named the carrier after him.