The "unrepentant sin" question is clearly part of the puzzle when welcoming the unbaptised into church membership. A reason why permitting this (even unwitting) disobedience would be more serious than others (e.g. an unwitting denial of the bible's teaching on the millenium) is that baptism itself defines who the church is.
Baptism defines whom we recognise to be members of the visible church, just as Spirit baptism creates the members of the invisible church. (1 Corinthians 12:13). People from both sides of the debate have agreed this. (See, for example, Thomas Shepard's The Church membership of Children)
When I became a convinced credobaptist aged 19, I don't think that I was approaching the subject from a historically baptist viewpoint. I saw that the New Testament commands people to be baptised upon their profession of faith, and that was enough for me. I failed to see the ecclesiological significance of credobaptism: that the church would strive to be a community of belivers only.
There are two relevant implications of the fact that baptism defines church membership.
First, To permit a conscientious paedobaptist into the church is to permit someone to belong to a church who has a very different idea of what a church is. In order to be a church together, do we not at least need to be able to agree what a church is? Is it (1) a covenanted community of believers. Or is it (2) a community that includes believers and their children?
Can we belong to the same church as those who disagree so deeply about what a church is?
Second, if baptism defines church membership it is going to be far easier for a predominantly paedobaptistic congregation to admit a credobaptist to membership (they believe him to be baptised). A credobaptistic congregation is going to have a greater weight on their conscience to admit to church membership one that they understand not to havec been baptised. In order to do this, they would have actually have to deny something that credos and paedos have usually agreed upon: that only the baptised may be admitted as members of the church!
Suddenly the move towards apparent unity requires disagreement on one of the things that we have previsouly been united upon!