The one time when my computer made noise whenever there was hard drive activity was when I accidentally shorted the hard drive LED pin and the case speaker pin at the front connectors on the motherboard... but given that your problem seems to have gone away without hardware changes, I don't think that's the case here.
As long as you don't get instability, there's no harm in underclocking, so enjoy!
Have you tried s2ctl yet? It could bring your idle temps even lower. The idle of my XP-M 2500+ dropped something like 4*C with absolutely zero impact on performance or stability...