Yeah i thought using the tweakguides method of disabling them, it would do this, but it still did the slight pause, so for me personally at the time using the method off the steam forum link, it did the trick for me. 
HL2 mega-stutter
- Thread starter Aod
- Start date
At least on an X2 core, and I'd assume the same to be true of a CPU with HT, forcing HL2.exe to run on only one core does definately help - otherwise it will randomly crash periodically. Sometimes ithing 5 minutes, sometimes within 30, but it invariably will.