Disabling Calendar Repair Assistant on mailboxes in Exchange Onprem 2019

Yes, it is generally safe to disable the CRA on Exchange on-premises mailboxes in a hybrid setup, and Microsoft's guidance in your case is sound. 
Here's a breakdown to give you confidence before rolling it out org-wide.

The CRA is a background process that periodically scans mailboxes and attempts to fix inconsistencies between meeting organizers and attendees, for example, correcting mismatches in meeting status, location, or time. It runs on a schedule and does so silently, without user action.

The problem is that in a hybrid exchange environment, this "repair" logic can work against you. When meeting update legitimately flows from Exchange online to on-premises (or visa versa), the CRA can misinterpret the state delta as an inconsistency and revert the meeting to a prior state, in your case, reinstating a cancellation that has already been superseded by an update.

This is a known behavioral quirk, not a bug.
It's an older article on the techcommunity explaining CRA
Exchange 2010 Calendar Repair Assistant | Microsoft Community Hub