I don't know enough about the mining industry to comment. But a properly designed external combustion chamber will be cleaner than any modern internal combustion engine. The NOX, CO, HC's, and particulates are bad enough, but there are more dangerous compounds beyond these.
About half the cost of automotive systems today is accounted for in the emissions controls equipment. If you think that's bad, check out the systems proposed for Diesels to meet 2010 EPA mandates for NOX, particulates, and other emissions. Caterpillar has already backed out of the U.S. market because of these mandates.
New emissions mandates will soon apply to small engines as well.