To disable certain job in rAthena just comment the job line from db/[pre-]re/job_db1.txt. Example usage to disable 2 Trans, 3rd, Babies, and Expanded for Ragnarok server.

disabling_job.diff

diff --git a/conf/msg_conf/map_msg.conf b/conf/msg_conf/map_msg.conf
index f4dfc46..ab14daa 100644
--- a/conf/msg_conf/map_msg.conf
+++ b/conf/msg_conf/map_msg.conf
@@ -753,7 +753,8 @@
 //Skill messages
 720: %s is required.
 721: [%s] Poison effect was applied to the weapon.
-//722: Free
+
+722: This job is unavailable.
 
 // @costume
 723: '%s' is an unknown costume
diff --git a/doc/script_commands.txt b/doc/script_commands.txt
index f42dd3c..1557d1b 100644
--- a/doc/script_commands.txt
+++ b/doc/script_commands.txt
@@ -4333,6 +4333,13 @@ See also db/[pre-]re/job_noenter_map.txt
 
 ---------------------------------------
 
+*isjob(JobID);
+
+Return true if JobID is available in the server.
+JobID is constant of Job_*.
+
+---------------------------------------
+
 *get_revision()
 
 This command will return the SVN revision number that the server is currently
diff --git a/src/map/atcommand.c b/src/map/atcommand.c
index fbbd570..89b599f 100644
--- a/src/map/atcommand.c
+++ b/src/map/atcommand.c
@@ -1048,6 +1048,11 @@ ACMD_FUNC(jobchange)
 		}
 	}
 
+	if (!pc_job_is_available((enum e_job)job)) {
+		clif_displaymessage(fd, msg_txt(sd,722)); // This job is unavailable.
+		return -1;
+	}
+
 	if (job == JOB_KNIGHT2 || job == JOB_CRUSADER2 || job == JOB_WEDDING || job == JOB_XMAS || job == JOB_SUMMER || job == JOB_HANBOK || job == JOB_OKTOBERFEST
 		|| job == JOB_LORD_KNIGHT2 || job == JOB_PALADIN2 || job == JOB_BABY_KNIGHT2 || job == JOB_BABY_CRUSADER2 || job == JOB_STAR_GLADIATOR2
 		|| (job >= JOB_RUNE_KNIGHT2 && job <= JOB_MECHANIC_T2) || (job >= JOB_BABY_RUNE2 && job <= JOB_BABY_MECHANIC2))
diff --git a/src/map/pc.c b/src/map/pc.c
index 7c939f0..8df6169 100755
--- a/src/map/pc.c
+++ b/src/map/pc.c
@@ -12187,6 +12187,22 @@ bool pc_job_can_entermap(enum e_job jobid, int m, int group_lv) {
 }
 
 /**
+ * Check if job is available or not
+ * @param jobid Job ID see enum e_job or sd->status.class_
+ * @return True:Available, False:Unavailable
+ **/
+bool pc_job_is_available(enum e_job jobid) {
+	uint16 idx = 0;
+	if (!pcdb_checkid(jobid))
+		return false;
+	idx = pc_class2idx(jobid);
+	if (job_info[idx].max_weight_base)
+		return true;
+	return false;
+}
+
+
+/**
  * Tells client about player's costume view on mapchange for checking 'nocostume' mapflag.
  * @param sd
  **/
diff --git a/src/map/pc.h b/src/map/pc.h
index acab411..c3ef62c 100644
--- a/src/map/pc.h
+++ b/src/map/pc.h
@@ -1294,6 +1294,7 @@ void pc_show_questinfo(struct map_session_data *sd);
 void pc_show_questinfo_reinit(struct map_session_data *sd);
 
 bool pc_job_can_entermap(enum e_job jobid, int m, int group_lv);
+bool pc_job_is_available(enum e_job jobid);
 
 #if defined(RENEWAL_DROP) || defined(RENEWAL_EXP)
 int pc_level_penalty_mod(int level_diff, uint32 mob_class, enum e_mode mode, int type);
diff --git a/src/map/script.c b/src/map/script.c
index 1d1c044..d35e500 100644
--- a/src/map/script.c
+++ b/src/map/script.c
@@ -22108,6 +22108,19 @@ BUILDIN_FUNC(openstorage2) {
 	return SCRIPT_CMD_SUCCESS;
 }
 
+/**
+ * Check if job is available in server
+ * isjob(jobid);
+ **/
+BUILDIN_FUNC(isjob) {
+	int job = script_getnum(st, 2);
+	if (!pc_job_is_available((enum e_job)job))
+		script_pushint(st, 0);
+	else
+		script_pushint(st, 1);
+	return SCRIPT_CMD_SUCCESS;
+}
+
 #include "../custom/script.inc"
 
 // declarations that were supposed to be exported from npc_chat.c
@@ -22703,6 +22716,7 @@ struct script_function buildin_func[] = {
 	BUILDIN_DEF(needed_status_point,"ii?"),
 	BUILDIN_DEF(jobcanentermap,"s?"),
 	BUILDIN_DEF(openstorage2,"ii?"),
+	BUILDIN_DEF(isjob,"i"),
 
 	// WoE TE
 	BUILDIN_DEF(agitstart3,""),