I can't agree with that. The speaker could omit "thou" and the imperative/plea would be obvious in the words "Be my vision." The word "thou" is used because the speaker is obviously addressing someone who is at a remove (or several.) What higher station could there be than being God? Consider, nearly every prayer is the same thing: an imperative/plea.

While your description of the durative "be" is correct in AAVE, the words are those of a traditional Irish tune and hymn. I'm going to bet that the originators of the tune and of the words, somewhere in Medieval Ireland, had no familiarity with forms of AAVE, which of course, did not exist at the time. The singers/speakers are implying permanence; they want God to be both their vision and to be able to see the world through God's eyes. We don't need to compare it to AAVE to see that.