Having this Krypto guy ordering people about in the world already sets him up as an obsticle to Superman whether or not he becomes Brainiac.
Not if it's handled in a way that he initially appears to be a benevolent figure, which was evidently the intent. After all, a similar story has already been told, as the premiere episode of the DCAU Justice League
series. In that story, Superman worked with Senator (and former astronaut) J. Allen Carter to execute a plan for global disarmament, which the world responded to positively (though with some dissenters). Ultimately it turned out that Carter was an alien infiltrator using Superman as a dupe to render Earth defenseless against an invasion. So it's not impossible that a story like this could be structured in such a way that Superman considered the character an ally at first. Again, it's important to remember that what we're reading here is only a secondhand summary of a rough treatment, and its handling of the tale doesn't necessarily represent the tone, approach, or level of detail that the hypothetical movie might have had. There's an enormous amount of room for interpretation here. (Indeed, realistically, there's no guarantee that the final movie would've borne more than the tiniest resemblance to this treatment. Very few preliminary treatments in Hollywood reach the big screen largely unchanged.)