I have nothing against this being about religion, but the thing is that if none of the viewers understand the message, then you did not do a very good job getting the message across.
I think the biggest issue is how you decide to illustrate, and word things.
I will shorten this into two simple problems, each falls into one of the above problems.
You decided to make the girl a princess, which you say symbolizes the everyday person. However, a princess is the exact opposite of an everyday person, a princess is someone who has a birthright to be seen as better than the average person. A princess is also associated with love as in romantic love, and the fact that she is looking for a prince only strengthens this. Why did you make her a princess? I understand that the two characters are much more fitting together if she is a princess, and they have mutual respect and all that, but this does not show kind and eternal Jesus-love, this shows love as in babymaking-love.
Another problem is how you word things in itself. I will focus on one statement, which is the last part when you said "what happened then is between the two of them", or something similar. The fact that you make what they did after "entering the kingdom" a secret, does definetly not hint to Jesus-love, but babymaking-love.
What I am trying to say is, if you take away the text you wrote about your thoughts behind the flash, all there is, is a story of a lonely princess realising that love has always been right by her.
You would have to be guessing a heck of a lot to get the same interpretation as you, and that is why I will simply ignore your interpretaion of the flash and review it for what it is.
-Story was all right, nothing I have not seen before. A bit cheezy too.
-Art was all right, not really a fan of the anime style you went for, can be really cool if done correctly though. It just looked a bit sloppy to me.
-Voice acting was ok, the same voice as all the flashes with narration on this website.
Honestly, it was just mediocre, and your description of it just did not fit.