Building an earthen wall around your portal will keep it from getting destroyed. Yes it takes time to build this but its better to waste an hour than waste weeks of work gathering materials and making gear. You can build small lodges and portal hubs on large islands that you intend to spend some time on and once you have picked every resource clean you can take all the equipment out and move it elsewhere and just abandon the structures if you don't want to waste the time deconstructing to reuse the materials.