Stab and Nowhere to Run only amounts to -5/-5. Sab-Sunen is a 6/6. So those cards combined bring toughness down to 1. Any damage Sab-Sunen has marked is irrelevant, since damage does not reduce toughness. Marked damage gets compared to toughness, and if it equals or exceeds the toughness, the creature is destroyed. But indestructible stops that. To kill an indestructible creature you have to bring the toughness all the way down to 0 or less with only -X/-X effects or counters. Damage does not help here. If the toughness reaches 0 or less, a different state based action can kill the creature, because it does not involve destroying it.

As a side note, neither Stab nor Nowhere to Run place counters, they both only apply a temporary decrease. Only effects that use the word "counter" use counters.