Yes you can deploy any package and scripts from ePO console. McAfee EEDK tool will help you.
First you have to convert batch file into McAfee deployment package with help of EEDK tool (packaging tool for creating ePO deployable packages). After conversion you need to check into ePO master repository where you can deploy it to machines.
For more information :https://kc.mcafee.com/corporate/index?page=content&id=KB74887&actp=LIST
Like ansarias said, you can use EEDK, but its not the easiest to setup.
Why not just use GPO or if you guys have a patching tool like SCCM?