Yes, it has been considered, but with some differences.
First, the inerting gas used is not helium - it's nitrogen. Nitrogen also doesn't support combustion, and is for practical purposes inert. It also has major advantages over helium in this role. For one, nitrogen is very close to air in density, and doesn't leak as easily as helium, so it's easier to retain.
Nitrogen is also much easier to obtain by separating air. It can be done on the ground with nitrogen carried in cylinders, or generated onboard with OBIGGS. If you were to use a more exotic gas, it would be halon, which also breaks the chemical reaction sustaining most fires.
In practice, inerting is only applied to fuel tanks, not to avionics compartments (which house the batteries). One reason is that inerting won't prevent lithium fires: the batteries already contain all the reagents they need.
Nitrogen would prevent a secondary fire, but another reason comes in play: avionics compartments aren't sealed. Fires in these bays, like in the cabin, can be addressed by the crew. This requires insulation for the lithium cells (as has been installed) and fire detection in the compartment to allow response before the secondary fire is out of control.
But, as the first linked paper states, it's certainly possible to improve on that with quick automated fire suppression. Aircraft safety design is a set of tradeoffs and it's an evolving field. It's possible that in some years, as the amount and importance of avionics inevitably increase, more weight will be spent on their fire protection.