I can't imagine that was the only time an Israelite was killed for breaking the Sabbath, just the only one mentioned. It was God's law to put to death those who broke it.
You're correct about intentional and unintentional sins. Only the unintentional ones were cleansed by the temple sacrifices.
I wouldn't doubt it that more Isrealites were killed for breaking the sabbath, I however contend that it wasn't some arbitrary type killing like "oh you picked up a stick! STONE HIM" type thing. I would imagine it was the mans intentions behind gathering the sticks which warranted his death.
Korah and his family were swallowed up for rebellion. Achan along with his family, were stoned for covetousness and lying. I think that these instances are much more severe since the individual along with their families were destroyed.
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