How to protect NTC thermistors for embedding in cement?
There are at least two main considerations: 


Protection against chemical effects. Some materials such as Portland cement are very high pH (alkaline) and that could attack the materials in the sensor. That also means that they are quite conductive in the presence of moisture. Since  you're probably using a high resistance thermistor, leakage could affect the reading, disproportionately so at lower temperatures. 
Protection against physical damage. The thermistor disk or bead is brittle under the (usually epoxy) coating. When the cement shrinks, creeps or flexes under pressure from outside it can transmit enormous forces to the sensor which could cause errors or damage the sensor. Silicone helps, but it is not compressible. 


Since you have such a thin layer it is difficult to protect the wire and sensor within that layer. You may be able to cut a deeper channel into the floor with a "diamond channel cutter" and insert a tube, however you will have to ensure there is sufficient thickness left over the water tubes or whatever is heating your floor.