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?
I love that whole section of John where Jesus is actually praying for us. That is so awesome. But unity does not trump truth, and in no way do I interpret that Scripture to mean that unity trumps truth.
Jesus also said that in the end many will say to Him "Lord, Lord...." and He will say to them, "Depart from Me, I never knew you." So clearly He knew that all who claimed Him would not truly know Him, but would rather be deceieved by a false gospel.
I do not believe that all Catholics are going to hell, but I do believe that Catholic theology leads there. To the extent that some Catholics have true faith but are misled or uninformed about specific theological points, I think it is possible for them to be true Christians. But if your faith is in your own effort to get you to heaven, you will come up short. And if your faith is in truth as given to you by a man -- albeit a great man called "Pope" -- then you also might be sadly misled. I say that not to hurt anyone. Most Catholics are wonderful and intelligent people who I am fortunate to know. But truth matters, especially the truth of the gospel.
Conflict, even in the church, can sometimes be a process God uses to teach and to purify us. It is not ideal, but then we are talking about imperfect people; and without the conflict we would likely never be challenged to understand the full counsel of God. Faith is more than a nice feeling.
We should be friends and allies on moral and freedom issues. That's it. We need to know where to draw lines.