Experience & avoiding incoming fire does count for a lot, and speed is useful for both offence AND defence where armour is only defensive.
I have plenty of ships that are fast at the expense of defensive hitpoints, and I am comfortable using them, relying on my wits to keep me alive. Personally I find I struggle to make effective use of an AFMU in time-critical situations but I know other Cmdrs make it work
It's a personal choice based on how willing the Cmdr is to compromise one stat for another but with the Chieftain I think thruster integrity is certainly something worth taking into account