Yes, dig and sell (or throw away) is the only way. Then, when they are somewhere you DO want them, block them from cloning by placing QR code clover, fences, or items around them.
I should probably do this but what I do is hold it all in my pockets until they can hold no more and then I throw everything on the beach; flowers, furniture, stacks of iron and stone, everything. I had beds next to toilets next to fishtanks and bug boxes next to fossils and pieces of iron, all next to each other in one big mess on the beach. It looked so beautiful. I also put a large number of trash cans in various spots all over the island so now I toss the less desirable flowers in there along with those annoying sticks that fall out of the trees every day.