I wonder what will happen to Vergo after he's been defeated (or escaped; depending on the situation). Smoker now knows about him so he's going to report him either way. Or will Vergo just call Smoker a liar and depend on his own reputation to keep his current position? He's higher ranked than Smoker apparently hence his words should weigh more. Something tells me that Vergo giving up his rank might not be very beneficial to Doflamingo and his grand scheme so I expect a rather surprising outcome at the end of the PH arc.
Like with Crocodile I imagine - Smoker will be left either trying to stop Luffy or keeping Ceaser and Vargo and the others under arrest. Smoker will then address the Marines and WG about the SH's and watch further cover ups or redirection about what happened.