You're right about "Kdo mě miluje?", which is more general, but both of them are correct.
Word order "Kdo miluje mě?" just emphasizes ME, as in "Peter loves Mary, Martin loves Susan, AND WHO LOVES ME?!"
That would be translated as "Kdo mě má rád?"
"Milovat" (to love) is stronger than "mít rád" (to like).