Just a "shower thought" I've had: is there any credence to the theory (mine) that ちゃん is a diminutive/"baby talk" form of さん (like when "ureshii desu" becomes "urechii dechu")?
Some preliminary research:
日本国語大辞典 has an example sentence dating from 1813: 「ばばちゃんいやいやと云ってだだをいふだ」. Dictionaries do make clear that it came from さん, but none of them list it as 幼児語 (baby talk). One reason this might be is that it has become a standardized way of addressing young children and female friends, so it is no longer considered 幼児語 as everyone uses it. This doesn't necessarily mean it didn't originate as 幼児語.
On the other hand, ちゃま (like さま but more intimate and childish) is listed as 幼児語 in all dictionaries I have checked, and the earliest example in 日本国語大辞典 is from 1900: 「ゆったり『慎ちゃま』と僕に云って」
Also note that たん is considered a 幼児語 version of ちゃん.
Considering the similarity between さん->ちゃん and さま->ちゃま, you might be right that this particular sound change, being characteristic of the way children speak, naturally resulted in more intimate forms of さん and さま.
I think more research would need to be done into ちゃん to be absolutely sure that it originated as 幼児語 and not from a dialect or other means. Origin aside, though, it is not labelled as 幼児語 in today's Japanese, and adults and children alike use it.