An alternate(and more common) verse of this stanza:
Now, Andrew had been married, and before he left his home,
Andrew and his wife together knelt in prayer before the Throne,
Asking God for His protection, and in the silence of the moon,
that not a Newfoundlander, would meet their water'doom.

is:

Now, Andrew had been married, and before he left his home,
Andrew and his wife together knelt in prayer before the Throne,
Asking God for His protection, that before he left his home,
to save him from the perils and, the dangers of the foam.

An Alternate take of this also exists, and I believe it is sung in the George Westcott version that I have still been unable to look at because I'm too drunk at the moment:
Whom the seas turned bottom upward, dashed against that rocky shore.
Her crew all clinging to her, thinking the storm would soon be o'er.
Andrew Davis was in trouble, looking forward to their ruin,
with the crew all hanging too her awaiting for their doom.

And in the bashing of the sea storm, the Rose in June went down,
Gliding softly toward the bottom, without a single sound.
In the stillness of the water, in the silence of the moon,
Oh, Every Newfoundlander Has lost a Rose in June.
Yes, Every Newfoundlander has lost a Rose in June.