Looking around, it seems the only thing one could use for cover is the contraption at the end of the hallway -- a long tube that probably is meant to withstand a lot of things, given its importance for the inner workings of this area. Still, it's at the end of the hall, past the moving sections. Sebastian's bombing has broken many of the spikes, making it far easier to pass -- although you would need to roll to determine how it goes.

However, judging by how the guardian up there stops attacking to move the hallway and try to set spikes into position for more hurting, it can't attack them and move the hallway at the same time. The bomb Sebastian throws falls and rolls away, exploding harmlessly over there.

If you could somehow manage to trick it into moving the place where it's at right now so you could reach it, or if you could attack it from a range and hit it, or if you could manipulate the area itself to your advantage somehow, you should be able to defeat it!