Coming from Halo: Reach, I remember when Bungie implemented a string of player level resets when it was found that players were afk'ing in PvE games (Firefight mode) for hours on end - they decided how to play the game yet were still punished for illegitimately gaining advantage over others by not actually 'playing' the game to rank up.
Now this isnt the same as the kneeling connectivity trick currently being used for Crota, but from the example it shows that Bungie have no worries resetting players who they think have wrongly gained advantage over others.
However with the current unease over the game itself from the community, resetting progress on a large scale would create yet more unrest that im sure they would want to avoid. I wouldnt be surprised that it will simply be patched, or if the problem is too complicated for a patch - that a statement will be issued warning players of a reset or a ban if they are found to be using the exploit.
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I guess that would indeed be a logical step for Bungie; patch and continue. At this point I wouldnd mind a ban that much; the endless grinding starts to get boring and I seem to have an endless beef with RNG.