Destroying the gates in order to change both future and past is impossible.
Future Rogue is already here, which means that A) destroying the gates didn't work, B) Plothole
Let's say the current time is moment 0.
In moment 0 they destroy they gates to prevent Rogue traveling back in time from moment 1.
If they succeed in destroying the gates then the gates will be gone in the future as well.
But Rogue was already able to travel back in time to a moment (-1) before the broke the gates, meaning that it didn't work or that Hiro didn't think it through.
The fact that Rogue is already here, proves that this plan can't work.
So:
-1 Future Rouge comes from the future
0 Destroy the gates to prevent Rouge from time travel
1 Without gates Rouge manages to travel back to -1
either it is this or there must be alternate timelines or universes. Maybe Edolas comes back in play again. If not Hiro should read more into time travel.