I haven't seen anything in game or lore wise that could punch through those shields it's hard enough for a MAC cannon. They can move planets all they want it's not going to stop them from being glassed.
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If you can generate those kinds of energy then you can most certainly punch through covenant shields, as we have seen they can be broken by 2 Mac rounds fired from a UNSC cruiser.
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If they had the weapons, they would've used them by now.
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Edited by Edcub One: 2/19/2016 8:18:05 PMWe don't know why they don't just bomb the city (the Traveler maybe?) but we do have varying stats for Covenant shields that goes from failing to modern nukes to withstanding extinction level attacks. So Destiny can fight them. Also they do have people like Oryx who can survive planet destroying events.