Nope, as far as I know and have experienced you don't lose rep points by helping the thieves, and if you finish Bloodscalp's quest and you play as a thief you will have the option to recieve your own thieves guild. Do know that the thieves are not the evil ones in the game but that Bodhi and her vamps are the evil ones, so Shadow thieves are for the good alignment and Bodhi's vamps are for the evil alignment.
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