Can the Orbital Sniper be used to kill units on a HQ? Is the HQ classed as a region as you can't move onto another factions HQ?
No, you cannot target minis in an HQ with Orbital Sniper. HQs are in general "safe" places for your minis.
An HQ is a region, and is considered controlled, and thus can be counted as such for any scoring opportunities of controlled regions.