Yes, as the pressure of Rome bore down upon Bar Kochba he began to suspect that the sages had turned on him and were looking to make peace with the Romans. This occurred after he became very arrogant and the sages began to lose faith in his piety.
After it appeared Beitar would be lost to the Romans, Bar Kochba accused Rabbi Elazar of being a spy and executed him. He then completely lost the support of all of the sages including Rabbi Akiva and they began calling him, “Bar Koziba” (the son of a lie) instead of “Bar Kochba”.
I am not aware of the Samaritans playing a role in the deterioration of the relationship between the sages and Bar Kochba other than the legend that it was a Samaritan who accused Rabbi Elazar of being a spy. There are records and papers written that support the view that the Samaritans too were forbidden to perform circumcisions, and that a pagan temple was built on Mount Gerizim. It’s unlikely that Samaritans would have been at Beitar the last stronghold of Bar Kochba if he hadn’t accepted them as part of his revolt and armies.