This has nothing to do with the differences in Guardian and Juggernaut as they're essentially the same, and everything to do with the companion each gets. Vette is about 35% better at damage dealing than the Droid and has a better selection for gear, making her an overall better companion.
In quest/solo play the Jugg has a clear advantage early on. But in 4 person flashpoints they both play the same and perform the same.
You're comparing a ranged DPS companion with a ranged Tank companion, of course Vette is going to deal more damage. However, T7 can be your own personal meat (or rather circuitry) shield and essentially double your HP pool.