Greg feels that the key structure is possibly confusing at the introduction:
The key is already ambivalent... Brian seems to believe it's in E (his statement about it starting on the major seventh is itself ambiguous; if the song is in E, what he means is that the verse part starts on the major chord of the flatted seventh, that is D major in the key of E. But when you add in that the intro starts on A, you have a song putatively in E where none of the parts start on the root, tonic chord). Looked at in isolation, this looks like a song in A is starting...
I disagree. The opening is a plagal motion of IV to I in E, which is a nice allusion to religious music (the plagal A-men at the end of hymns). This certainly makes sense, given the title of the song. The I - ii - I motion at the end of the introduction (E - F#min - E) is unusual in standard tonal progressions, but it also makes sense as an altered form of the plagal cadence, with ii standing in for IV. This plagal motion also occurs at the chorus, appropriately accompanying "God only knows what I'd do without you." The verse starts on bVII (D), alluding to the blues heritage of Rock-n-Roll. Quite often the V - IV - I progression in blues is translated into I - bVII - IV in rock (see AC/DC's "Back in Black" for a good example). But in "God Only Knows" the subtonic chord is not part of a blues progression. Instead, the bVII moves to a minor dominant (Bmin), giving a modal feel. It does not make sense in the key of D as Greg suggests, but it is definitely not stable in E major either. The following F#min - B (maj) progression brings us clearly to E major. This segmentation follows a reading of the lyrics. The unstable harmonies in the first verse accompany the negative opening, "I may not always love you," which switches gears suddenly to reassure the listener that the singer really does love him/her. I love the imagery evoked by "as long as there are stars above you." I visualize night-time, eternity, stars swirling around a lover's head, endless love. This switch of mood coincides with the switch to stable harmonies in E major. The same switch occurs in the second verse, "If you should ever leave me/life would go on, believe me" versus, "The world could show nothing to me."
The distinction between doubt and certitude is not as clearcut as I am making it, though. One could read the lyrics as being about a somewhat bitter lover. The first verse starts with the warning already mentioned. The other three lines don't necessarily refute that warning, as the "it" is somewhat ambiguous. "It" is usually interpreted as "my love," but it could refer to "not always loving you." Then the chorus becomes an exclamation that the singer could have been much better off out of that relationship: "God only knows what I'd be without you!" Verse Two could be read in a sarcastic tone: I can't believe you would ever get up the guts to leave me (though I will be just fine if you do, thanks!). Then the break could be a daydream about freedom, with the modulation to A major as his feint towards a simpler life (fewer sharps). The repeat of the second verse includes an obbligato that seems to mock the idea of giving up life for the worthless lover, made even more explicit in Petra's version (she laughs for this obbligato). Listen to 1:45 in both versions. And the final stretto could be a conversation between the lovers, as they both believe their lives would be improved without each other.
What's beautiful is that both interpretations can exist side-by-side. Little details complete the beauty of this piece: the little skip in hypermeter at the end of the second chorus, the "fractal" plagal shape (keys of E - A - E, introduction and coda), the counterpoint of the break, and the great timbral colors. I've now listened to the Petra version eleven times and the BB version 3 times since yesterday. Obsessed? Yeah, a little.