The ability will trigger only if Kjeldoran Home Guard is still on the battlefield at end of combat. If it’s been dealt lethal combat damage and destroyed during that combat (or has left the battlefield during that combat by any other means), its ability won’t trigger and you won’t get a token.

You put the Deserter token onto the battlefield even if you can’t put a -0/-1 counter on Kjeldoran Home Guard (because it left the battlefield after its ability triggered but before it resolved, for example).