The newest version of Greenify (3.4+) will identify some "background-free" apps in Greenify as "No need to hibernate" and not hibernate them by default. Background-free apps should hardly impact the battery consumption or device performance. Still you can force the hibernation by manually hibernate it once and tick "always ignore background-free".
"Running in background" does not mean it has definite impact on battery consumption or device performance. Experienced developers can also reduce the memory footprint of background service as low as several megabytes, which is negligible in most middle-to-high end devices with 1~2G RAM.
"May slow down the device" also does not mean it has definite impact on device smoothness. Android caches the process of apps regularly run, thus significantly reduced the cost of launching it in background.