There is an answer to that question, why doesn't 29th century Starfleet stop Nero:
They still can.
In a very real sense, they have plenty of time.
But what if Nero's time travel escapade alters the future to the point where there is no time agency, no temporal accord and no Relativity? How do we know for certain the Relativity is safe from time alterations?
We know their *ships* are, so it stands to reason that their entire organization is as well.