They don't attack you on sight, but you have to enter the guild through the ratways like you did in the beginning. Karliah explains what happened and that Mercer is a lying bastard, they check the safe with all of the guild's goods to find that she's telling the truth, that Mercer is a bastard who stole everything from the guild and is for the most, the reason for it's slow death.
If we're talking about when you chase after Karliah.
Lord Hard-on wrote:
I think he means if you go back before that.
There's really...no possible way to do that. When Mercer tells you to "give Brynjolf my regaurds" it's after Karliah shot you with a poisioned arrow. After that Karliah nurses you back to health and the quest to shank a Mercer starts, which includes the pardon for you and Karliah.