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? if it was indeed safe then every time time travel has taken place no matter how tiny a new time line will be created (the butterfly effect) and a new Relativity would be created. By now there must be 5000+ Relativity's existing.
The only logical conclusion I can come up with is that Nero's time travelling re-writes the future and to the new future Relativity Nero's time travelling is a must.