You can. The question is, how well do you want to hide the faction

1) Easy
#To simply hide the faction:
(faction_set_note_available, ":fac_30", 0),
2) Medium
#But if you want to completely disable the faction, you have to do something about the range kingdoms_begin, kingdoms_end:
(try_for_range, ":kingdom", kingdoms_begin, kingdoms_end),
You can move the faction outside of that range, by adding a global variable:
kingdoms_end = "$g_kingdoms_end"
where you define "$g_kingdoms_end", based on a script.
Downside is, that you can only disable/enable the last faction, not a faction in-between.
3) Great
It should also be possible, to completely get rid of (try_for_range, ":kingdom", kingdoms_begin, kingdoms_end), by using a troop as a list, where you store all existing and active kingdoms inside the troop and then just iterate through that troop. That way you can disable any kingdom.
For details, check out Lumos list script. It's pretty cool:
http://forums.taleworlds.com/index.php/topic,8652.msg6845772.html#msg6845772