The topic of the Nine can be a touchy subject for some guardians. I mean, they are invisible magical planets that have an unknown amount of power and goals alien to our own. At least with the Hive gods we know we can kill them with enough concentrated firepower. We can't even hurt the Nine unless we are willing to remove all life from the solar system then blow up a few planets.
This especially annoys the Vanguard, the control freaks that they are. If the strategy of "throw teams of six at a problem until it stops breathing" followed by "steal everything shiny that's not nailed down" fails to resolve the issue, then they try to use bureaucracy. They try to keep us from associating too much with them. "Don't talk about classified information around Xur or the Emissary" this and "Don't trust trust the Drifter" that. I'm pretty sure they are the ones who got the Trials shut down too, but that's a conspiracy theory at best. Not that it matters anyway, considering they're probably omniscient.
Personally, I think that having them around is in our best interest. Aside from the fact that I support peace and friendship with anyone not actively trying to murder us at this point, from a utilitarian perspective, they need us more than we need them. If we die, they die. If they die, nothing happens to us. Of course, they are working on that and I wish them the best of luck, but for now our interests are required to align. And considering every other species that we've encountered has actively tried to murder us all upon first contact, that makes us practically best friends.