How deep will you fish comfortably for smallies?  Will pulling them from very deep areas kill them?

I'm going to fish a very clear lake in MN with good structure 40-60' deep, but not sure how ethical it is as a conservationist.  I do know to bring them up slow

I wouldn't be that concerned.  You'll kill plenty of fish by gut/gill hooking them, and it's also good for the overall population to harvest some of the fish out of there anyway.  Smallmouth are very hardy fish.

Smallmouth can start showing some signs of barotrauma around 20 ft, with a sharp increase at just over 30 ft. Once you reach 60-70' it becomes a catch and keep game because most will die without immediate attention (fizzing). Playing them slowly does nothing except possibly make the situation worse. Get them up quick and then try and immediately release them so they can swim back down. 

From reading many articles on this topic.  It is best, as others have said, is to boat them as quickly as possible and then send them head first into the water giving them a little push to get back down.  I do not fish for SMB deeper than 20-25' down.  They may be in deeper water but they are usually suspended where I fish.