First the judge is oging to look into the bias allegation raised by Stone's counsel.

Second, it is not up to the judge to pick the jury (or exercise challenges to jurors) -- that's the lawyers' (and therefore the client's) job. The jury foreman's background was well discussed in the jury questionnaire and the voir dire process, and Stone's lawyers didn't think it was a problem. During jury selection you usually have the right to request a juror be stricken for cause (like bias, etc), and you also have the right to strike a limited number of potential jurors for just about any reason (peremptory challenges). Stone didn't request either.

Third, every day in America, GOP jurors pass judgment on Dem defendants and vice versa. Party affiliation -- even passionate party affiliation -- does not without more suggest partiality on the facts of the case. And to the extent you think someone is not going to be impartial,. then you strike them during jury selection -- which Stone did not.