Is supplicating for the disappearance of pimples from the body considered a rejection of Allah's decree, and will this affect future marriage?

What you mentioned is not an objection to Allah's decree; rather, it is part of taking the legitimate means to achieve legitimate goals, such as supplicating with grace and perseverance. Taking legitimate means—and supplication is one of them—does not contradict faith in divine decree and destiny, for means are part of Allah’s decree. Allah has commanded us to be eager for what benefits us and to take the means for the betterment of our worldly life and the Hereafter, and supplication is one of the greatest of these means. Do not worry too much about its effect on your marriage, and strive in supplication for Allah to grant you both happiness and affection in your marriage.