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The Citadel Concordance says:

The sept of Lordsport was also destroyed by Robert Baratheon's forces, but unlike the stronghold of the Botleys and the village it was never rebuilt

This squarely lays the blame on Robert's forces (Which is curious, given that the bulk of the Royal Forces were followers of the Seven, but that's not the point of the question.)

The ASOIAF wiki makes no mention of the forces responsible:

During Greyjoy's Rebellion, Lordsport and its timber and wattle keep were the first places on Pyke to fall when King Robert I Baratheon and his forces landed on the island. The keep and the village were razed and the sept was burned to the ground.

The cited chapter itself does not make any mention of who destroyed the sept:

When last he’d seen Lordsport, it had been a smoking wasteland, the skeletons of burnt longships and smashed galleys littering the stony shore like the bones of dead leviathans, the houses no more than broken walls and cold ashes. After ten years, few traces of the war remained. The smallfolk had built new hovels with the stones of the old, and cut fresh sod for their roofs. A new inn had risen beside the landing, twice the size of the old one, with a lower story of cut stone and two upper stories of timber. The sept beyond had never been rebuilt, though; only a seven-sided foundation remained where it had stood. Robert Baratheon’s fury had soured the ironmen’s taste for the new gods, it would seem.
ACOK - Theon I

This only mentions that the town was burnt and the people rebuilt it, with the exception of the Sept. So why does the Citadel blame Robert's forces in no ambiguous terms? What proof do they have that it was Robert? Given that the Faith was barely tolerated in the Isles and Balon only fanned the religious/ethnic tensions before and after the rebellion, it is entirely possible that the Ironborn may have done it themselves, to send a message of sorts that there was no place for New gods on the Isles any more.

Who actually burnt down the sept?

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As far as I can see nothing explicit has been said either way in canon material apart from the quote you link. The problem with that is it can be interpreted in one of two ways.

Robert Baratheon’s fury had soured the ironmen’s taste for the new gods, it would seem.
A Clash of Kings, Theon I

  1. Robert's forces had burnt down the sept and the unhappy Ironborn took it as an opportunity not to rebuild a new one.
  2. The Ironborn, already unhappy with the Faith, took their opportunity when Lordsport was burnt down and burnt the sept.

The Citadel page on The Botleys of Lordport mentions the sept being burnt down but points no fingers.

The old sept of Lordsport was destroyed in the rebellion, but it was never rebuilt.

However, lacking an explicit quote of who it was I think we can assume it was Robert's forces. The Citadel and the wiki both seem to assume that's the case too which strengthens the point.

It's worth noting though that even in today's times when a fire get's going it's very hard to stop, put that back into medieval times and it's next to impossible. Considering that the whole of Lordsport was burnt to the ground and had to be rebuilt I think it's safe to assume that Robert's forces burnt the sept whether intentionally or otherwise. If this is the case, and with the Ironborn unhappy with the Faith, it's safe to assume if the flames did catch onto the sept they probably didn't try to stop them.

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