As I recall, there was actually a specific mandate from Ted Turner to not allow the Planeteers to use any kind of violence against the eco-villains.
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http://www.turner.com/planet/mission.html
Interestingly enough, the site also goes into some of the reasoning behind why the eco-villains were so caricatured and over the top.
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Actually this doesn't really excuse them that much. Leaving aside the argument that laying the blame for pollution at the feet of outright supervillains kinda undermines the supposed educational value of the show, did they really have to be such lame supervillains?
I mean dear lord, how the heck is anyone supposed to take your radioactive monster seriously when he's running around in a mohawk and Hawaiian shirt?