EventSentry doesn't really interact with any running processes by default and running our agent shouldn't result in any compatibility issues. If configured, EventSentry would potentially read a log file generated of your backup software, but all other activity is directed at the OS (check service, disk space, performance) and not at the actual running software.
What backup software are you running, and what exactly does "terrible" mean? High CPU usage, does it take longer?
Have you contacted the vendor of the backup software?