I assume that you mean the raid with Vitamin. Do you mean that Freedom turn hostile immediately after your final conversation with Vitamin (where he gives you your 'reward') or was it at some other point? Is it just the Freedomers in Warlab, or all Freedomers everywhere?
Did you accidentally shoot any of the Freedomers while clearing out the dogs? Otherwise I don't know why they would turn hostile toward you. Or why Sid can't help. You may need to replay from an earlier save.
You may be able to turn the Freedom faction back to 'neutral' by entering freedom in the [ESC]+[F] 'Attitude' menu. However, I don't know if this will work given that Sid is unable to change them. (If freedom doesn't work, you could try svoboda, which is Russian for freedom.)