Well, I still think industry would tend towards machines. Machines don't get injured as easily, and they don't sue you when they do. In addition, the relative rarity of thugs would be prohibitive - and using Allomancy 9-5 every day could have culminative effects on you - consider pewter dragging. This applies for Lurchers and Coinshots as well - there are just so many things you could do with those powers that are enjoyable that it would take a huge amount of money to tempt them to act as human electromagnets for monorails. I can see something like that happening in a authoritarian imperial reign of fear, but I doubt that's going to happen again on Scadrial.
For pigeonholing - absolutely. However, I can see specialist "Allomancer Corps" operations springing up - companies that use Allomancers and Feruchemists for contract work - or special departments in public service. Of course, the application of the magic is wide enough that you could probably find academic work even as a thug - I'm imagining pewter-dragging to work on a thesis. You know, piles of white powder everywhere, scribbling furiously.
Emotional Allomancy - that could be a problem. It would be something to conceal from birth, for certain.