Yes, X-Files tackled conspiracy theories too. And in much more complex fashion (until season 5 at least). Still, I can't see why HL story can't be analized in the same manner.
Well, in the 90s possible implications of ecological catastrophic changes were rasing more consern then now, that's for sure. But that doesn't mean that the topic is lost its meaning completely.

But the Tiberium infestation is something that isn't caused by any human actions, unlike climate change, deforestation etc. It just happens (isn't it insinuated in some of the games that it's caused by aliens who want to colonize earth?), without any human responsibility for it. So it's hard to see it as a relevant analogy for real-life ecological issues.

Apparently you haven't watched all the cut-scenes. Tiberium did originate from aliens. But it was Brotherhood of Nod that made it spread so quickly. There were even people in GDI (like Dr. Moebius) whe wanted to exploit the infestation to their own ends, disregarding any potential danger (including earth becoming uninhabitable for humans). Just like in real life people who stumble on things they barely understand try to use them without thinking of consequences. It is too of a general and common situation really.