Well, from what I've seen, you could complete the mission just going after Raiders and intercepting whatever nukes pop up. As mentioned in a different thread, Basestars aren't much of a threat neither in Diaspora nor in the show.
I'd say that in-mission reloads would be a good idea for R2. You could touch down in the flightpod, get rearmed, perhaps slightly patched up and take off again. This would allow much longer and more intense missions which would normally cause you to run out of ammo. Also, remember that a combat landing and rearming takes you out of battle for a while, so this wouldn't be a game breaker.