Give them a high static level based on their rank. But not so high as to rended the PC's role in the MQ redundant.
I.e,
PC lvl 1:
Guards, lvl 10
Captains, lvl 25
PC lvl 20:
Guards, lvl 25
Captains: lvl 35
PC lvl 40:
Guards, lvl 25
Captains, lvl 35.
etc etc.
That way, you're not going to [censored] slap them at low levels and you've got a useful counterpart if need be later on.
The issue with the Battle for Bruma in Oblivion was that the enemy's level scaled differently to the guards. So if you were a High level the guards were gimped. If you were a low level you really had to question your roll in the MQ. It is the most ass backwards way to scale levels they could possibly had conceived. That said I still love the game.
There is an easy fix to this.
Don't scale the enemy's.
Have more, stronger, different monsters and opponents to encounter with varying skills, levels and equipment. Simply giving an enemy 15k HP isn't making it harder. It just means he who posses the most HP wins.
One thing I will say though. Is it made sense for the Guards to get slaughtered in the battle for Bruma, if they didn't, why were we even needed??