I've never been able to beat this game without thinking "Yay! I saved Earth! I blew up Naju! ...including all those cute Blue Landers who sold me all those power-ups. Doh!"
Think of it this way: at least you were able to save the ones that you collected as power-ups. *shrug*
What was the alternative? Appeasement? Anyway, keep in mind the BL's knew exactly what your mission was. (How could they not? They'd already seen someone else make the attempt; it's the one who left the message in the first room.) And they knew what their fate would be once you succeeded. Apparently they preferred death to a lifetime in the service of wickedness. So remember their sacrifice, but also remember that they did so willingly.
So did the safeties over the self-destruct mechanism reset after the guy who left the Apocalyptic Log died? Are the corridors for any purpose other than locking the self-destruct mechanism? If not, then where are the living quarters? (Maybe it's just that those aren't important to the plot, but it still bugs me.) If so, then it would suck living there, wouldn't it?
I'll field this one. Yes, living there would suck if you were human. But aliens built this place... we have no idea whether their species ever needed to sleep or eat or use the toilet. Given they built a giant planetoid and all the biomechanical enemies laying around, it's an easy guess these guys made a lot of progress in transhumanism, too (or rather transalienism), and thus maybe they evolved beyond the need for living quarters. As for the corridors, they probably also served as storage areas for important keys or weapons (considering you get one every time you beat a corridor). And I don't think it's inconceivable that the self-destruct mechanisms might reset after a while if you don't get them all. Or maybe they were reset by the bad guys (from the weapons they use, at least some of them must be sentient).
It also really bugs me that whoever left the log said "I don't have much time"...yet he had the time to leave us those notes. Maybe if he didn't stop to write everything down, he could have blown NAJU up and saved us the trouble...
I dunno, that didn't seem that weird to me. Obviously, our Apocalypse Logger was seriously worried that he might fail (justifiably so, as he did fail), so I don't blame him for leaving behind instructions for someone else to try if he didn't make it. Even with as primitive a device as a word processor, that log could only have taken a few minutes to think up and write, at most. Rather, it was MUCH stranger that all his messages were in English, when his race never had any contact with humanity.
The only thing that really gets me is why did the final boss, "It", attack me after Naju was blown up? Wouldn't it have killed it to try to stop me at the very end of the boss rush instead?
Maybe it just got back from the store. "Dum-de-dum-dum, got myself some cake fixings. Red-Opto is gonna love this... wait, WTF? WHO BLEW UP MY HOUSE?!"