If you have decided to deploy one version of the agent to some systems and want to leave others "as is", no problem at all. In fact this is pretty common in the enterprise. You will be able to deploy from one branch of the master repository while deploying another version from yet another branch. The client (system) is only as good as the version installed. So keep an eye on new agents and what they fix and decide accordingly on an upgrade of the agent version on any system(s).
Thank you very much. I haven't had a whole lot of experience with two agent versions so I didn't want to try this and be completely wrong about the ability to do it.
Also make sure to update the extension for the McAfee agent to the latest version you are using in ePO. Extensions are backward compatible, and you must have the same version of the extension as the latest McAfee Agent package. If you only update the package and not the extension, you might run into some issues. Extension = to latest package checked in ePO.