Ideally, you shouldn't have to punish your PCs with fluff hammers for making optimal tactical decisions and using their Powers in combat.
You say punish, I say complicate.
I believe that consequences should play a big part in Scadrial. Also, that which makes for the optimal tactical
decision may have consequences that make it a poor strategic
decision. Stereotypically, Keepers appear to choose long term benefits over instant gratification.
Lives are on the line, after all, and the player can only guess how much use of Feruchemy will draw the ire of the Inquisition. For that matter, so does the Narrator.
Is guessing necessary? I always thought it could be summed up as any overt use of Feruchemy. In fact, you later state that "a Keeper so much as breathing is [a concern to the Lord Ruler]". Exposure pretty much means death, likely with the secondary purpose of granting Hemalurgical benefits to a Steel Inquisitor.
Beyond that, what kind of horrible game gives you cool powers but then doesn't let you use them or punishes you for using them?
Again, I look at it less as a punishment and more as the consequences of overt actions by certain hunted individuals. It's part of the package: You have the potential for near-limitless power, but if you are caught using that power, you're going to be in for a world of hurt. There is a rather large organization obsessed with killing people like you. If they discover your identity, you'll be on the run for the rest of your life. Act accordingly.
Nevertheless, what you might do is roll for the investigators to see if they can identify the work of a Keeper or Mistborn.
Great idea! Especially if the Heroes catch wind that a group of Obligators has been dispatched to investigate their last foray. Then the Heroes could try to create false leads and all kinds of other problems for the investigators.
Ratchet up the opposition accordingly.
Right! I look at "opposition" as more than putting antagonists in a direct (physical?) confrontation with the Heroes. I believe the other suggestions that I made could be viewed as "Ratchet[ing] up the opposition", too.
So, I believe we are rooting for the same side, just approaching from different angles and using different cheers. Maybe?
Oh, and Brandon offers a suggestion for Narrators having problems with Feruchemists using Steel in combat (page 312), which ties nicely into my observations on consequences. Hope that helps!