Currently, I think that allowing them to be "wasted" points is a better option than not.
Besides that, it affects spawned units, principally from a tervigon, but also "grown" units such as scarabs. I would rather these units not be worth "free" victory points, particularly at the same time fortifications are penalized. (waiting for Keith to pipe up.......)
Counting killed rather than "still alive" takes care of both problems nicely......and I also think that was how VPs (sorry, my 4th! ed book is at home) was supposed to work originally....I think Sam saying it's on the table points was just a mistake.
I'm much more interested in what people have to say about the non-tertiary objectives as those are the least likely to change.
I don't think you should just have just Big Guns Never Tire OR The Scouring (they need less unwieldy names), I think you need both. However, I see nothing wrong with one of them being a secondary. They could even be primary and secondary on the same mission, or different missions, which I think takes care of you worry about finding something to do for Mission #2 secondary.
I would also like to see The Relic be a primary, if possible. Ben's amendment of only being able to pick it up turn 2, is fine, though I think he's mistaken in think that the units that can do that are a "loophole", tons and tons and tons of units are capable of grabbing the Relic first turn, including any unit with a rhino.
Actually, no, I'm not so sure we should make that change.