Why kill them? Barad's gonna doublecross you anyway. Also, the monks aren't evil. Just do the eight chambers (at 2300 hundred xp per) and head on to the Udnerdark (expect company when you open the second door).
However, to answer your question, no, the other NPC's in the game won't come after you if you kill the monks.
Dunno about that walkthrough you read, but my understanding is that the only way to end up fighting the monks is to start the trouble yourself.
Nightowl2
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