I can't say too much about Samui; haven't dived that area in more than a year now. Last time I was there divesites like Sail Rock were in good shape and I didn't hear, see or notice anything unusual while diving.
I'm pretty sure the Thais will clean the aircraft before scuttling it. One of the guys in charge of the project (Khun Paitul) has been an active environmentalist for more than 12 years now and is an Instructor himself.
Yes, other ways of creating reefs are possible but do not immediately create an attractive place for divers (or marinelife). I've dived over reefballs, hundreds of car tyres, concrete poles and white star-like structures that supposedly will grow coral on them but have most of the time been disappointed with the lack of scenery and marinelife on them.
Large, metal structures like wrecks and planes seem to thrive with creatures in very little time and are fun to dive on.