"Always" because getting infected forces an alignment change.
Of course, for "natural" weres this justification goes right out the window...
I've never been real happy with the listed alignments for weres. Wolves are more "lawful" than rats, IMO, yet werewolves are CE and wererats LE. Basically, the listed alignments come from fiction. Werewolves are usually depicted as ravening bloody berserkers, hence CE. The wererats in the Fafhrd & Grey Mouser books were cunning and organized, hence LE. Beorn in the Hobbit is a nice guy, so werebears are listed as LG (though personally, I'd peg Beorn as more CG).