1) Can you discard military cards to get a +1 while colonizing or is that only during aggression/war?
No. discarding for strength is only for aggressions (you cannot play cards for strength in wars at all, BTW)
2) And does playing a +2/+1 military card count against your total number you can discard to get the +1 bonus?
Yes. The total number of cards you can play in defense is limited to your number of military actions, regardless of how they are played.
Edit: Darn. ninja'd