The point is that no one knew what the thing even was. They assumed wrongly on all fronts, so all of their actions are valid as based off what they knew they moved accordingly to try and prevent it.
I disagree, the Agents are all Heroes. Trip may have died but that doesn't mean he's the only Hero, especially since his death will be like Skye's "Uncle Ben" moment in a sort of way that will push her to be better and not to let his death be in vain.