glow stone effect active when it got kill?

No — if Glowstone is killed before your Ending Step, its end-of-turn effect won't fire at all.

"At the end of your turn" is a triggered ability on the gear itself (Rule 383.1), and it only triggers while Glowstone is on the board. Once it's in the trash, it can't trigger — so no "kill this," and no 5 damage to your units (Rule 383.2.c).

One caveat: if Glowstone is killed by its own end-of-turn ability, that's different — both instructions ("kill this" and "deal 5 to all units you control") are part of the same resolving ability, so the 5 damage still happens even though it just killed itself (Rule 359.3.e.14.b).