Yeah, the closest I can think of for semi-recent stories has been in Aaron's Thor, where that new SHIELD agent Roz is part of the environmental SHIELD department or something. Ive never thought about it, but given the political/social underpinning of the MU, its sort of surprising they haven't dug into this topic more.
I wonder what the rights to Captain Planet are like right now? I'd laugh my ass off to see Marvel try to update and incorporate that character into the 616.
Oh! Maybe Zen the Intergalactic Ninja! He was an environmental character too right? Never saw the cartoon but I did have an old Game Boy game and he was always fighting smog monsters and stuff.....