As you say, the absence of a question mark in a sentence otherwise structured as a question indicates the speaker's or writer's expectation that the person or persons addressed will cooperate with or acquiesce in or obey the instruction being given. The Chicago Manual of Style, fifteenth edition (2003) refers to expressions of this type as "courtesy questions" and offers the following advice on how to punctuate them:
6.74 Courtesy question. A request courteously disguised as a question does not require a question mark.
[Examples:] Would you kindly respond by March 1. [and] Will the audience please rise.
But "courtesy question" is a bit of a misnomer, since these statements are really something closer to "courtesy demands": The speaker or writer expects that you will perform the requested action and expresses the request in the form of a question only out of politeness.
It seems to me that adding a question mark to this type of question invites (that is to say, accepts the possibility of) a negative response in the way that ending it with a period does not. Therefore, when you are dealing with someone who has greater authority or a greater claim to deference than you do—an employer, say, or a parent—it makes sense to include the question mark simply as a token that you are not arrogating to yourself the right to tell that other person what to do.
Under the circumstances, your concern that "using a question mark [might] bring a sense of rudeness" seems unfounded, since posing the request as a real question (and not as a "courtesy question") is logically a sign of respect, not of rudeness.