Pure Good with a military win ?

Goodness is only affected buy colonization event and planetary event, not by the means used to get a planet. Using Terror star to destroy system won't affect your goodness rating.

And how will the Good win the final fight against Evil, if their are denied to have a military win?
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It is the easiest combo to win with, in my opinion.

If you play the standard alignments then you generally end up joining with the Altarians and Torians. Whereas evil tends to fight seperately.

Once Paladin ships come along it gives you such a big advantage over the evil civs.

After the evil civs are gone you can then turn your attention to your former allies This has no bearing on your alignment.

I have found the Torians generally pick up treachery faster than the Altarians as they dont tend to allow Transports to camp in their sectors. You will get the "we are better off dealing with you first..." message if their forces are stronger than yours.