If the CTA doesn't offer any prayer to Karmapa Ogyen Trinley, it clearly shows that they themselves don't believe that the Karmapa Ogyen Trinley is the real Karmapa who supposed to be the emanation of Chenrezig. If they believe the Karmapa is Chenrezig, regardless of what, they will still offer prayer. This is very basic.
CTA is not a real democratic government, they still rely on Nechung to give them prophecy and guidance. If they chose to believe in protectors or deities, then they must also believe that Karmapa as a Buddha will never make mistakes. Therefore they should continue to respect him regardless of what he did. If they don't, means that they don't believe, then why recognized him?