No. John didn't say to imagine no god,. Just no religion. It is and extension of his assertion that The Beatles meant more to kids than Jesus Christ, which was true, in which he says how much more loving life could be. As a performer he tried to carefully walk that line after the album burnings. That scared him.

Why not

Maybe it was, maybe it was not, but we can use it as such. And why should the churches have all the best songs ?

It’s just a damn good song. We don’t have an atheist anthem, but if you want to think it is one you can. If I had to put money on anything, I’d bet that John Lennon was an out and out atheist even if he’d never written the words to this song.