Kurama didn't feared it. Kurama hated it. Big difference.
Plus, in Kushina's case it was more special. Her body had undergone through pregnancy, bijuu extraction and whatnot.
Who said that she died because of Bijuu extraction only?
The context of the two is highly different.
But still I feel he would rather wait than undergo reconstitution via death.
Well compare the two scenarios and compare the STATE of each Jinchuriki:
Kushina: Strength enough to stay concious after having the full kyuubi extracted, strength enough to reason well, strength enough to do what no other shinobi in her Era could do, Suppress the Kyuubi for a time. Likely to live if she had not been killed by the claw. Enough chakra left to be sealed within Naruto, chakra that was capable of suppressing the kyuubi for a while longer.
Overall it seems to me that her strength was not waning in any massive way.
Naruto: Chakra exhaustion, battling for days, likely hungry. Previously injured. Mentally taxed with maintaining chakra shrouds. Madara likely ripped the chakra through his connection to each chakra shroud of the SA leaving only Yin shrouds behind. Not conscious in any way, So low on chakra his heart can no longer beat on its own.
Overall it seems that his chakra level is far far lower than Kushina's were when she died. And Naruto would have died if not for Sakura massaging his heart.
Chakra is an expression of the bodies strength, physical energy from the cells, and the spiritual power or will of the user. The fact that Kushina still had so much chakra to use indicated she would have survived. Naruto on the other had may have the will but his body is failing him.
It was their decision to die by sealing away Kurama in Naruto. That doesn't mean what they did is the only way. btw, they weren't morons. They chose the right decision to save the village.
Right decision considering their own specific knowledge. Ultimately it seems it was ignorance on their parts that lead to their deaths. IE idiots.