I do not see the fragmentation as a bad thing. That's what keeps us challenged to stay true to the teachings of Christ. Too much unity amongst fallible humans tends to lead to all of them following false teachings (in the church) or a deceitful leader (in government). There is one church and she is scattered among many denominations. I think we are facing a time of testing and purification right now. I think there will be a big separation in the church, a reorganization. God is cleaning house. I am not a prophet and I don't speak for God, so that's just based on human observation. But there are some big things happening in churches right now. Big changes. And most are not for the better. A lot of this has to do with weak humans wanting to feel good about themselves and others more than they want to honor and glorify a holy God.
If you believe that Holy Scripture is inerrant and that it is inspired by the Holy Spirit, then you **must - by definition** believe that the words I quoted from the Gospel of St. John are true and accurate. It says that Jesus prayed to the Father that we all might be one. If these words are taken literally - and I don't know how else they could be taken, because it is very clear - that means He places a high priority on union. Are you going to argue with Jesus by saying fragmentation is not bad, when He has very clearly said - 5 times! - that He desires union?