Well Barney owed Church because Church wanted the control of the island back. The island produces cocain and is used by the CIA (maybe to gain money from it and finance black operations).
In "The Expendables 1" Barney kills Munroe whichwho previously killed the general. Munroe was a EX-CIA Agent. Besides the fact that Barney kills Munroe (whichwho may have cooperated with the CIA), he he plunges the military regime too. This fact makes it impossible for Church to get the control back over the island. If the military regime would be still there, he could possibly promote a new general and take him under his control.
Hopefully this will answer your question.