In Nanoha, the power levels are fairly high (think about a Mahou Shoujo version of Dragonball or Gundam), so the replacement of a major character is a fairly serious problem too.
For a direct example, the mission "Legendary Illogic", by Firemagic and me. Basically, a Replacement!Nanoha, after being completely drained of her magic power, still managed to survive being struck by a very powerful lightning-based attack. (And by "very powerful", we mean "we had to basically resort to the most powerful combination technique we had while wondering if it was actually plausible for PPC Agents")
About Madoka, our only hope is that nothing exits from pre-Madokami Madokaverse (exceptions made for recruits, of course).
Especially Kyubey. Although the nursery problem can be easily solved by making Kyubey-hating Agents make surveillance turns. If he just keeps being shredded on sight with extreme prejudice and without being able to get near potential magical girls, he will reach the point where he will think that going after Nursery teenagers isn't cost-efficient, right?
After all, one of the reasons why he didn't give up on Madoka when Homura started going after him is because he had found a golden-egg-laying hen. Enough energy to fulfill the planet's quota and maybe even more in one go? Homura probably would have had to make his entire race extinct to keep Madoka from being pestered by them.
Ah, and Annihilation Lightning is stated to be LETHAL with a direct hit. And it took up most of the magic that Ari grabbed from around Hogwarts, and the magic from draining Harry and Not!Nanoha, plus ... more
I now know how EVERYONE feels when me and Himosheep start Hetaliaing (can that be a verb?) at everyone. And... hrm. If we're going with Dangerous Canon Entities, I raise you Ramuthra or Nouda from... more