Not at all.
About the same time that philosophers were claiming that the sun was a ball of hot gass, Apollo was first made into a sun god.
Apollo is not a sun god in Homer or any mythological text . The son god is Helios son of Hyperion, much worshipped on Rhodes and the myths told of Helios are very different than the myths told of Apollo.
Rather, the philosophers tried to rationalize the gods: Zeus became the heavens, Hera became air, Poseidon became water, Demeter became earth, Hephaistos became fire, and Apollo became light and enlightenment and as such could be conceived of as the divine force behind the sun.
Similarly Aprhrodite/Venus was connected to the male god Eosphoros or Phosphors or Hesperos who was the god of the planet that today we call Venus.
So religiously Apollo was connected with the sun and Aphrodite/Venus was connected to the planet today called Venus, and some religious connections were made with other deities with the other planets and the moon, but even religiously no-one ever believed that Apollo WAS the sun or that Aphrodite WAS the planet Venus.
And Helios continued to be worshipped also. The idea that he rode a chariot though the sky just became understood as a religious metaphor.
The sun god in Rome was even, for a time, made into the head of the Roman pantheon. See http://en.wikipedia.org/wiki/Sol_Invictus and was quite distinct from Apollo who was also worshipped in Rome and elsewhere. Yet every educated person, at that time, knew that the sun itself, was a ball of fire.
One can’t get rid of religion so easily. The religious person will just start talking about “religious metaphors” and “divine truths that can only (or at least mostly) be understood through such metaphors.”