If the contractor did this poor a job on the concrete, I'd almost bet he/she did not put a shower pan liner underneath the concrete, either. You will need some type of liner underneath the mortar bed (they range from rubber the copper). Mortar beds are concete, and concrete is ultimately porous. Even if you tile over the mortar bed, there is still always the possibility that the moisture can seep through the grout (even "sealed" grout), migrate down through the mortar bed and settle into the subfloor (definitely NOT a good thing). You need some type of waterproof material between the bottom/sides of the mortar bed and the subfloor and base of the side walls to prevent any moisture damage to them should this type of seepage occur. Talk to the staff at your local home center, or get on-line and check out shower pan liners... you'll be glad you did. Good luck.