Indexing a barrel is semi normal practices during a barrel install on civilian rifles.
Standard spec for the military is the rear sight has to be within 13 clicks off center to be acceptable. A target shooter want the rear sight to be dead center since cranking the windage knobs is standard practice, and with a dead center zero, to have a known return windage point to come back to.
In regards to your question/concern, a simple test to confirm that the bolt is not binding is to do a 45* drop test or just stick you finger in the back of the carrier and feel if the bolt lugs and the extension lugs are binding on pass threw.
As a general run for re-indexing, if you can zero out the rifle with the rear sight (even if all the way over to one side), then you should be able to index the barrel without problems. It's when you have the rear sight cranked all the way over, and you still not zeroed that chances are you will end up rotating the barrel extension in the upper barrel socket too much, and have lug binding or the feed ramps just way rotated to allow a clean feed.
As for shimming or using the leather mallet, both work fine, and it just boils down to how much time you have on your hands and if you plan on shimming, to have the tools needed to pull the barrel.
Myself, I shim all my match rifles at barrel install (read get the gas port TDC) and then use the adjustable front sight to fine tune at the range live fire zeroing. As for my service rigs (at this point in my life, the rigs I try to burn up on a yearly bases), they get the leather mallet since sooner or later the rifle it going to take a hit anyway. Plus, I'm not up for the multi re-indexing/shimming game that you have to play to fine tune between trips to the shop and the range (like a perfect zero really matter when your busting/burning up rifles on a fixed FSB anyway) .
Hope this answers your question.