Denominationalism entails separation, which is not good. Therefore, it is not ideal and should not be, unless unity would result in even greater evil.
The divisions between denominations, if legitimate therefore, implies that joining together would result in sin. The division between Presbyterians and Baptists is probably the best example of this. A Presbyterian by conviction is one who believes that not bringing one's infant children for baptism is sin. It is not just an option or something good. It is mandated by Scripture. A Presbyterian by conviction must see the Baptists' denial of infant baptism as sin, as is their practice of what he sees as re-baptism. Just because they profess the true faith does not mean that therefore they are not perceived to be sinning in their denial of the inclusion of children in the Covenant of Grace. A Credobaptist by conviction similarly sees the Presbyterian affirmation of infant baptism as robbing the child of making a profession of faith, and giving rise to the possibility of false assurance of salvation, and thus it is sin. Both sides see the other side's position as entailing sin, and thus the necessity of differing denominations.
If however, one church does not see the position of another church as error and sin, why is there a division? In fact, that is one grievous error of Congregationalism (and independent Baptist churches). Those who reject connectionalism (the necessary but not sufficient precursor to Presbyterian church polity) are guilty of schism against the Body of Christ, for why aren't they seeking to have at the very least fraternal relations with churches of like faith, and try to work towards the unity Christ which we already have in Christ (but is not fully visibly realized now)?
Denominationalism is not ideal, but it is the best arrangement given our finite knowledge this side of glory. The alternative is some version of tyranny or anarchy, neither of which glorifies God.