In retrospect, the cringeworthy of that scene might have stemmed from the awkward delivery and audio direction rather than the writing itself. It might have helped had they worded it differently, like "Are you sure?" or something entirely else, but the way that Meer phrases the line makes it sound unintentionally hilarious -- Either Shepard was pulling a very inept con or the dialogue assignment was ****ed.
Well meant generally terrible lines, but yes that line was due to some awful voice direction, like with Ashley's...uh...reaction. Jacob had a good ones in ME3 as well. But anyway, that's aside.