The constitutional provision quoted in the question has been interpreted to require that a jury trial be available to a person accused of crime by the US Federal Government. Then accused is free to waive this right, and be tried by a judge only if s/he so chooses. The accuse is also free to waive the right to a trial altogether, and plead guilty (or "no contest" which waives a trail without an admission of guilt).
The provision could reasonably be interpreted to require that if there is a trial, it be by jury. But I don't see how it could reasonably be read to require trials in all cases, and forbid guilty pleas.