Is a Muslim sinful for granting a Christian colleague an hour off weekly to go to church, with these hours to be compensated for later, just like his other colleagues who are granted similar accommodations for other purposes?

The ruling on helping a colleague depends on the work regulations and the terms of the contract. If the colleague is entitled to the leave or facilities mentioned, then there is no harm in allowing him them, regardless of his purpose. However, if the questioner has the right to deny them, then he should not assist his colleague in falsehood.