There, the Kingpin reveals to Osborn that Spencer Smythe did not die in the explosion back in "The Spider Slayer", but that he escaped early on before the explosion ensued at OsCorp and was met up by the Kingpin. But rather than killing him outright for his failure with the Spider Slayer's goal to kill Spider-Man, the Kingpin sees that he may still have some future use for Spencer, so he places him in chronological suspension.
In this context, the Kingpin's decision to spare Spencer Smythe's life is motivated by a desire to retain his usefulness, rather than eliminating him outright. This leads to Spencer being placed in a state of temporal stasis.