It is certainly true that the comedic convention of disguise used in the play provokes both laughter and discomfort. One example of discomfort can be seen the moment when Feste agrees to disguise himself as Sir Topas, the curate, in order to diagnose Malvolio as being mad.
This scene particularly causes discomfort for several reasons. For one thing, the audience well knows that Malvolio isn't really mad but rather being made the object of a cruel and pointless joke. Since we know he isn't truly mad, we also sense that his punishment of being submerged in total darkness is especially cruel, particularly because it is a form of torture. Hence, when Feste agrees to disguise himself as the curate to try to trick Malvolio into believing he is insane, we can really feel Malvolio's pain. First he tries to trick Malvolio into seeming to be insane when Malvolio asks him to "go to [his] lady," meaning go to Olivia with the purpose of notifying her of what has happened, but Feste twists his words and accuses him of talking of "nothing but ladies" (IV.ii.21-24). Then Feste continues to trick Malvolio into looking insane by insisting that Malvolio is not in a dark room at all. However, he denies the darkness by twisting his own words in a way he knows Malvolio will not understand, as we see in Feste's lines describing the dark room Malvolio is in:
Why, it hath bay windows transparent as barricadoes [barricades], and clearstones [high windows] toward the south north as lustrous as ebony; and yet complainest thou of obstruction? (34-37)
Since Feste has just likened the non-existent bay windows to barricades, which create darkness, and described the non-existent high windows as letting in "ebony," or blackness, he is actually affirming that Malvolio is in total darkness. But of course, as Feste would expect, Malvolio is too dimwitted to understand his meaning and merely continues to insist that he is not crazy and that the room is dark. However, these two speeches in which Feste twists words make Malvolio seem like he is crazy when he is not, making the audience empathize with Malvolio as he is in such a terrible state.