It was always far easier to tear something down than build it up. Since it was just destroying the Helicarriers, Tony had much less to do.
All he needed to do was indicate where the self-destruct devices might be.
When the three carriers attacked each other later, these locations couldn't be touched.
Hence, he had to do his best to dismantle them.
Some useful components could be kept, like the intact Chitauri equipment.
Away from the carrier's programming, it was impossible for these things that were left behind to self-destruct.
It was safest to tear down such a huge Helicarrier.
Also, if they were turned into scraps out in the wild, it would be useless even if Hydra blew up. Blowing up some agents and opponents wouldn't make any sort of impact, let alone cause chaos.
This time, Tony needed to fly half an hour to get to the carrier.