Ah, but if you're looking at the intent, rather than just the plain language of the Amendment, then you'd have to agree that there is a "Wall of Separation" between church and state.
If he wanted to "settle the great question of citizenship", he could have done so with the language of the amendment. He did not, or rather in failing to specify, he did but didn't define it in the manner he intended.
To me, the language is plain. Adding the authors thoughts behind those plain words removes any interpretation. As others have said, it would have been simply inconceivable to these men that this country would sit idly by while being invaded by the millions. Therefore putting too fine a point on the issue somewhat silly.
The "wall" is another issue entirely. Not referenced in the constitution, only in one man's correspondence to another. When one researches the circumstances surrounding the letter, and reads the original unedited letter. The "intent" of the phrase becomes likewise quite clear.
More here:
http://www.usconstitution.net/jeffwall.html