Having watched the National Geographic documentary on the expeditions into the caves, the chances of external contamination for the samples looked acceptably low. The samples were taken from an inch or more inside the crystals, from liquid inclusions accessed by drilling with sterilized drill bits and sterile transfer. The sample sites were in deeper areas of the cave to further reduce the risk.
Combine that with the lack of a close genetic match to modern samples, and the level of confidence in the samples been uncontaminated should be satisfactory high. To contaminate the inclusion, you'd have to breach it, contaminate it and the crystal would have to regrow (something it doesn't do when out of water) all deep inside a cave so hot that it can kill in a couple of minutes without protection.