He didn't need our will or running to decide that scheme. Despite the ramifications of that scheme for unbelievers, including for unbelieving Jews, He had the prerogative to decide upon His own scheme. He decided it on His own.
If it was left up to man to decide the scheme upon which salvation would be granted, many would have decided that Jewish ethnicity should be the basis upon which salvation should be granted; others were asserting that Law-keeping should be the basis – but God, without requiring anyone's permission, will, or running – decided upon His own scheme: salvation would be granted by grace through faith alone.
That's all Paul was defending in Romans 9. The scheme (salvation through faith) was God's and God's alone. And despite the ramifications of this scheme for unbelieving Jews, God was just and His promises had not failed. Their faith in the Gospel was on sure ground despite the taunts of the Judaisers.