I only said that where it all started is when the Vortigaunts did the most damage at that time of the incident as that's the point of origin of the Resonance Cascade. By the time portal storms were raging throughout on the planet, assuming the Vortigaunts were freed by then, they were most likely trying to survive/get into hiding and still don't even pose a threat to humanity if they wanted to.
If anything people are more afraid of is the other Xenian life and infestation (and then eventually the Combine). Without a doubt, they (not the Vortigaunts) did most of the damage and killings. And as I stated before, it's not only just time and their low kill count of humanity that contributes to why humans are friendly with vortigaunts. Both are going through the same shit, both share the same enemy, both share the same goal. Them being aliens doesn't matter anymore. Because of this they work together and even formed friendships over the years. Not just a few years, or one decade but nearly two. And considering after all those years, humanity is bound to learn at some point that the vortigaunts killings were not of their own free will. Eli, who has experienced the horrors of where it all started, is friends with them.