You mentioned your frame is aluminum so all of the rust must have come from the bottom bracket cups or spindle. Be careful cleaning the frame's threads so you don't damage the relatively soft aluminum, clean the bottom bracket cup threads and spindle thoroughly and grease or anti-seize treat the threads and spindle copiously before reinstalling them. As an alternative Teflon plumbers tape can be used on the bb thread to assure a good seal and prevent corrosion.