I don't know about the alarms thing, but the loss of reputation is explained by the fact that there is a quest that involves the Temple of Lathander later in the game.
The game is pretty forgiving like that. If there is an area you need to enter to complete a quest or two, you can often kill everyone in the building without loss of reputation. I suppose it makes the game a little easier if you happen to make a mistake.
<< Spolier >>
I know you can do the same thing in the Order of the Radiant Heart -- kill a dozen Paladins without reputation loss. Maybe it's that way with all of the temples. Have yourself a nice little Chaotic Evil killing spree

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"The supreme irony of life is that no one gets out of it alive." Job: A Comedy of Justice