Firstly – I don’t think you could seriously criticise SY for having a negative impact – they have consistently championed the unknown and publicised the obscure, particularly through their own labels.
Albini’s criticism is of the fact that they made the to move to a major based on their own needs, but influenced other bands to do the same thing and acted as “enablers” for major labels to sign bands who weren’t suited to that milieu. I don’t necessarily agree but it’s a valid viewpoint.
Albini performing a recording job for an artist signed to a major is very different to encouraging an indie band to enter that kind of relationship. As mentioned, his policy has been that he is happy to work with anyone who pays the asking rate. The money was higher with Nirvana or Bush because of the high level of incidental hassle of dealing with the label itself (viz the wrangling over In Utero). Had he wished to bilk the label he would have held out for points on the recording instead of a flat fee.
Hats off for telling GQ that he hopes the magazine fails.