On Sunday, I confessed along with my brothers and sisters in church that I believed, among other things, in the "holy catholic church". Of course, being Protestant, I understood that this meant the universal church, not the Roman Catholic Church. I also understood it to mean the church, as comprised of the elect, and not the various manmade institutions referred to as "churches" or sometimes as "the church". I have never had a problem distinguishing between these two concepts and disregarding the temporal institutional form of the church when making this confession. I believe that in a spiritual sense the church is both holy and universal notwithstanding the disunity of organized Christianity.
An argument can be made that the apparent disunity of organized Christianity is a terrible witness to the world and that the appearance of disunity is confusing to seekers and a basis for claims of hypocrisy by critics. Accordingly, I agree that it is important to work toward ecumenical unity and harmony among Christian organizations.
On the other hand, I have often seen calls for unity used as a cudgel to enforce conformity to the narrowest and most confining point of view. The faction which seeks to impose its intolerant or restrictive point of view on the institution threatens schism with those who decline to adopt their point of view and then accuses them of creating disunity for failing to fall in line. For example, if I advocate an open and affirming stance toward homosexuality, then I am the one who causes disunity by refusing to go along with the homophobic faction's declaration of what is permitted belief. For them, I must confess that Jesus is Lord AND hate gay people. It is not enough to confess that Jesus is Lord. If I declare that the form of baptism is subject to a high degree of freedom, those who are otherwise inclined will decry my heresy and accuse me of creating disunity for failing to see the light as they see it. I must confess Jesus as Lord AND totally immerse adults only.
In my view, unity and conformity are two different things. If I confess Jesus as Lord, surely I have a sufficient amount of common ground with others who also confess Him as Lord to work together with them to advance the Kingdom without agreeing with them about every detail. If I love my brothers and sisters, surely I will be willing to accept a pretty wide range of points of view just as I accept a diversity of personalities and gifts. It's only when I claim to be some kind of an authority on spiritual matters and insistent on conformity that I become intolerant and divisive.