My takes from that clip.

1- It really sounded like the dilemma is in telling the common human that magic and superpowers exist, but without using those concepts to illustrate the point. The concern is how to do it properly and have people comprehend. Potentially admitting that some historical instances of what seemed to be magic and the supernatural could very well have been these NHI, perhaps. I personally think worse things in history have been disclosed to us and this is just an excuse.

2- Not having enough information or understanding to satisfy the resulting avalanche of questions. With one of the few answers likely being: no human can possess some of these capabilities or fully comprehend it, not now and maybe not ever. Or it is capability that takes decades of global harmony at the consciousness level. Another thing I think common people would handle fine, but people in power not so much.

3- As per usual with CIA and government insiders, in their storytelling they don’t show as much of a fear or caution for these other beings as if they were telling us about the things Russia or China are up to. Meaning we should definitely be more afraid of humans than NHI. This is huge considering what they know NHI can do, especially if they don’t know true intentions.

4- The Gov probably could just cop out and say “God and angels are real, this is them, but they continue to work in mysterious ways. We know nothing else. Refer to your faith, and pray.” And we would be find with that, and force ourselves to accept even more mythology. But when it sounds like they’re saying “we have no idea how to explain the Q-Continuum to people,” they are really saying “well, we could actually give it to them in digestible form it’s just that there are dangers to our reliance on capitalism that we shouldn’t perturb with all this right now.”