I haven't run cgminer-gekko without minera, but my guess is that there would be no actual difference (other than usability). The mining itself is handled by cgminer.

Minera is just the management application. It makes it easier to change the config (if you like GUI interfaces over config files) and it provides a nice summary of statistics in a nice looking web GUI. It also takes care of things like starting the miner at boot, auto starting if it crashes, and stuff like that.

But under the hood it's still just cgminer running under screen.