There is a more pedestrian explanation.
Legal documents of the Constitutional period regularly capitalized nouns, in the German style. This practice continued thru the mid-1800s, when it was dropped from the stylebook. Thereafter, the distinction was between proper nouns (capitalized) and common nouns (not capitalized) -- as is the practice today.
If you go back and look at the wills, deeds and land transfers of the Constitutional period, you'll find that nouns were generally capitalized. After the Civil War, they were not.
Style changes it seems are quite arbitrary, depending on the political necessities of the day. I note that the dictionaries arbitrarily decided to re-write the definition of marriage, removing any reference to male-female unions. Very timely for the Mass. courts, who used the occasion to stamp their approval on same-sex marriages.
All dictionaries, especially the legal dictionaries, always defined marriage as between one man and one women.
Same sexers now have a source to legitimicize their 'unions.'
I imagine Congress found it a godsend to realize they could call their new subjects 'citizens.' Heretofore, they were unable to because the capitalized word was reserved for Sovereigns in the U.S. Constitution prior to the mid 1800's, as you point out.