The Keepers are neutral guardians of the dimensional realms. When an object is taken that should not be in mortal hands, their sole objective is to stop you because they do not know what devastation a human could unleash with such artifacts. But once the characters show effort to aid the Keepers/drive off the evil, the Keepers will guide the crews. And very much so. Being corrupted does not seem to help much at all.

For instance, the Keepers in Shadows of Evil attack us because we are holding onto the Summoning Key, obtaining relevant items to our characters in a purgatory version of their original city. Those Keepers only wish to stop us from aiding the Shadow Man (whose intentions were unknown to us) Once you reach the latter steps of the quest, however, they help us to eradicate the Shadow Man from this realm.

In Der Eisendrache, the Keeper only attacked us because it was corrupted. By Richtofen using the Vril Rod, the Keeper (before corruption) set out on a mission to obtain the energy of zombies using elemental forces in order to stop the evil (Groph).

In Zetsubou no Shima, Nan Sapwe was depicted as a Keeper himself and sacrificed his own head to be used as a weapon against evil. Again, for us to take that ancient artifact no doubt made the Keepers want to protect it, even if it meant attacking us.

It's not to say that they aren't intelligent - in fact, there's no doubt that they probably hold the wisdom of the entire lifespan of all universes. However, they are simply neutral in that they are here to maintain balance in the multiverses at whatever means necessary, and for this reason, the keepers must be the true good guys of the story.