Situation: Wrestler A disagrees with the official's call, gets in his face and makes contact or even pushes him. The official immediately signals flagrant misconduct on Wrestler A (disqualifying him), who then refuses to shake hands with Wrestler B (who wins by disqualification). Wrestler A's refusal to shake hands is of course unsportsmanlike conduct.

I know A's team is deducted two points and B's team is given 6 (for the DQ), but should A's team be deducted another two for the UC? Should the dual meet be held up until A comes back to shake? Can A even be called for unsportsmanlike given that he was (just) disqualified and therefore is supposed to be removed from the premises?

Since you just hit him with Flagrant Misconduct and removed him from the event, I wouldn't look to have him shake hands after the bout.
Since you stated that his team loses 2 points and the opposing team gets 6, this would be a dual. Np use penalizing the team further, this is an 8 point swing.
At least with the coaches I know, I would not want to be that kid at the next practice.

Practically speaking, A is gone and can not be punished further from a wrestling standpoint. Depending on the severity of the contact, this could be assualt on a sports official.
Refusal to leave could be tresspass or criminal tresspass.