You could try using an acid wash on the brick and mortar. This should be available at a masonry supply retailer like County Concrete. One that I use is called 600 Detergent. I've never used it to take paint off of bricks, but it might work because at my company we use it to wash recently laid bricks that have dryed mortar on them. It's a very potent cleaner so you will want to dilute it with water. About an inch of detergent in the bottom of a five gallon bucket and fill the rest up with water. You need to wet the bricks with water before you start to wash, otherwise they will absorb the detergent and shorten their lifespan. I recommend wearing rubber gloves and using a heavy duty nylon brush or a brillo type pad to scrub the bricks. You will want to rinse the brick soon after scrubbing it, again, to avoid absorbtion. If you are worried about water getting everywhere, use a wet dry vac.
If you want to use rocks, I would suggest gluing them right to the brick using an epoxy type substance and then you could use mortar to fill in the joints, or you could just glue them really close together.