You'll have to clear away the rocks in order to kill the weeds at the roots. DO NOT burn or start a fire to kill them. The rocks and even the plants you want to save need to be removed. once removed you'll need to hand till the soil in order to get to the roots. Once all this has been removed and the soil removed, you'll need to repot the area using landscapers mesh cutting out just those areas around the plants you want to save. You'll then need to create a bed using fine mulch before you fill with the garden rocks.
The pavers will need to be lifted up in order to extract the weed at the root. Once you've exposed the root area then use the weed kill at the roots.