Service disruptions could be minimized by doing the following....
I'd hate to see what "not minimized" looks like.
Convert all stations from Queens Plaza to Main St to B division standards. ...and then... Run Broadway service on the newly converted line west of Queeensboro Plaza. Close the section from Queensboro Plaza to Times Sq completely.
There's not enough room on the Broadway Line to take in all of the Flushing trains, in addition to the Broadway trains already there. To say nothing of adding about 1/2 hr to the commutes of people heading to the east side of Manhattan.
Of course this plan would still be disruptive....
Yeah, you could say that! It would be "easier" to build a new tube under 42nd St, and make the Flushing line 3 tracks from end to end. Not that that'll ever happen, but it would sooner happen than what you're proposing.