To borrow a quote from History.
"Well, when the President does it, that means that it is not illegal."
So just because someone/thing sings off on something, doesn't automatically make it legal.
If the orders came from the Federation Council, it means a majority of members likely voted to move the Ba'ku.
Or that the council just authorized Dougherty to negotiate with the Ba'ku on the subject and Ru'afo somehow convinced him just flat out move them as a time saving measure. That might explain why it didn't take Riker long to convince them to review the decision, of course their so called allies shooting at their flagship in an unprovoked attack might have also had something to do with it.