I believe yes and these are the reasons:

1. Paul urges to pray for all people specifically for those in authority and pope of Rome has a lot of authority among living people as the spiritual leader of the largest religious organization. Catholics believe in the Bible and even I disagree with some interpretation I still belive that works through their imperfection. So having a pope that can bring spiritual biblical change within the body of Catholics is important not only for Catholics.
2. You pray for those you love and you began to love those whom you pray about. I have been almost always in environments in Albania where Catholics and Orthodoxs has been regareded as church members without the salvation. It seemed to me and I belive it still among many evangelicals that the only saved people are in some evangelical churches. I have good friends who are Orthodox and Catholics whom I really respect for their faith and devotion to the Lord and the Church. This doesn;t mean that I will have services together with them, but I’m talking about the heart.

These are 2 main reasons that I believe we should pray for these events that God’s will to be done as it is in heaven. Even we don’t see immediate answers from our prayers  we should continue to pray until Jesus comes back to restore everything. In that time he will come for a church without blamishes and spots. Until that time we should clean our sports even it is hard to see alone.