Hyperthreading causes a single core to do twice the work in "theory". It allows two threads to be ran on a single processor simultaneously. Disabling HT can drop core temperatures in normal use; but when there's a max load it really doesn't vary all that much in my experience. Stress testing with IBT shows almost no difference in thermal output.
And as dragonsamus said; stock cooler isn't a good overclocking option. It may hold a small overclock but absolutely has no chance of pushing that thing to 5Ghz per core. You should start looking into aftermarket cooling if you're wanting to go that way.