After reading all the comments (a dirty job, but someone has to do it), I reach this conclusion, which doesn't require any massive changes to our justice system:

The constitutional right to "confront" a witness against you should be interpreted as the right to run your own unbiased tests on any dog whose results are used. This would mean a neutral handler whom the dog doesn't know conducts double-blind tests on the dog. If the dog is found to be unreliable by the judge, then the evidence is discarded, the same as if a warrantless search had been conducted.