"God Gave Rock and Roll to You"
While listening to this, I started wondering if the musical phrase to which Rod Argent sings "To ev'ry boy He gave a" is a scale. The first note (F#) is doubled, but otherwise it is a section of a D major scale:The next word in the phrase ("song") drops to an A note, discontinuing the scale.
While I was thinking about that, I also started wondering if the "ev'ry boy" part of that lyrical phrase is a reference to the "Every good boy does fine" mnemonic for remembering what notes go on the lines in written music (in treble clef, at least). It seems to fit because both that phrase and "God Gave Rock and Roll to You" are about music. Furthermore, that musical phrase is a scale (the same sort of thing that would be learned along with that mnemonic), and it begins on the last of the lines in that mnemonic. But I'm not confident that it's a reference.
"Be Glad"
At about 6:28, there's this phrase in the piano part (I think I have the notation right):
It occurs again at about 7:22 (after the line "Your soul, your voice, your freedom"), lowered a whole step so that it starts on Bb.
I'm surprised I never noticed before, but it's very similar to the first phrase of the tune "Antioch":
Both are diatonic descents that start with the same rhythm. "Antioch" is the tune to which "Joy to the World" is sung, so the lyrical connection of "Joy" and "Be glad" is there too.
As I mentioned a couple years ago, Rod Argent quoted the hymn tune "Cwm Rhondda" in a live version of "Hold Your Head Up" (on the Encore album, which was released about a year after In Deep), so there's precedence for his borrowing and altering hymn tunes. (Maybe precedence isn't the right word though, since "Be Glad" pre-dates that quotation of "Cwm Rhondda").
As I realized only recently, the next song on the album - "Christmas for the Free" - quotes the phrase "Joy to the world," which seems to suggest this was an intentional borrowing and not just a coincidental resemblance.