The gain in AF speed on the 300 2.8 Vs the 100-400 is substantial. Even with a TC on the prime.
The 300 2.8 has second generation IS Vs the first generation IS on the 100-400.
With the 100-400 you must turn off the IS on any rest. That's a major disadvantage.
The 300 2.8 is one of the few lens's that excels with the 2x TC offering a LOT more reach.
Canon lens prices are climbing rapidly and the new 300 2.8 MKII is going to send used MK1 prices higher.
There is almost no chance at all a buyer will loose money on a used MK1 right now which is why I suggest it as an option.
Buy it, use it, sell it.
Cranking up the ISO is the last resort from my perspective.
Either way the 100-400L is still a great piece of glass.