Newcrons are pretty terrible, yes, but what I hate most about that codex is that they completely ignored a perfect chance to introduce factions and simultaneously avoid completely retconning the previous lore (C'tan Loyalists vs Independent Lords).
To return to the original topic: The SSoE having a dedicated military arm doesn't make a lot of sense, but they definitely do have agents they hire to do wetwork or prevent it (see Black Mountain and The Burning Life). In fact, just today I had an idea for some player-generated fiction that would require some Sisters interference...