The expression, as used in this text, is borrowed from a later, corrupted usage common in late Classical Arabic. It is better understood if referred back to its original usage.

The earlier usage is

فلان مات صبراً

This simply means that he died in prison. It could mean that he was imprisoned for life, or simply expired while in prison on a lesser sentence. If the latter was meant, there may be a hint at poor prioson conditions or even positive abuse.

The word صبر is a synonym for حبس

Extending the latter meaning, a slightly modified expression appeared later
قُتل صبراً

This meant that the prisoner died in prison, but not of natural causes (the cause may be torture, abuse, neglect, or extra-judicial killing)

In time, the new expression acquired a different meaning: that the prisoner was held pending execution (put on death row, as we say today, and then was executed).