Well, as far as i remember breaking the arms and elgs of someone turned to stone just means you would have to hold or join the parts together again before brining the person abck, else he/she would come without them. And they do not break, but separate the limbs from the main thing, just to make sure they won't be having the best of a legate just by stumbling upon the place. It is kinda pointless eince the legates can use the regenerate spell too, but that is a 7th leve spel, meaning a much harder thing to have on hand.
The Healer heroic path is not truly a loophole, for he can use raise dead on a subject dead for up to his own level in minutes, menaing at least 19 in this cae, but not quite as powerful as raise dead, for example.
As to legates pulling people back fromthe dead, Nightfall, well, they can, but the person has to be willing, that means the resistance dead are safe of being brought and kept prisoner by the Order of Shadow, not much else.
Also, sincec the raise dead of the healer is from the heroic path it is considered innate magic, meaning it cannot be detected by an astirax. Not an ubber power for a 19th level character anyway, as said earlier.
The rule on greater schools is realy that one, it costs 2 spell energy more than the spell level, this can still be reduced by spell talismans or any other mean, and note that in 2nd edition access to the greater schools is possible from level 5 instead of the 1st edition 7th level. The rule on the greater cost is on page 123 of the 2nd edition book under the Greater Spellcasting Feat description.
One thing they made quite a mess with is the explanation of spell energy and the magecraft feat, I even think 2nd edition made a worse job than 1st had done.