Back when Drexler penned Engines he was primarily concerned with the grey goo scenario, to which he came up with the active shields concept. He's since toned down his fears about grey goo: http://www.crnano.org/PR-IOP.htm
As for the potential for pollution, Drexler has made it clear that nanotech will do more good for the environment than bad: http://www.spiritofmaat.com/archive/feb1/n...