How can I alternate stopping the spinning disk and the fans?
As mentioned in my comment, your best bet to reduce noise would be to migrate to a computer with an SSD drive or replace the drive in your existing computer. The noise from a standard hard drive is highly variable, while the noise from a fan set at a constant speed with fan control software would be white noise. 

In regards to turning off the fan entirely, that would be risky as the Mac not only has tight tolerances that allow heat to build up quickly when the fan is off, but the OS on Macs has regular cron jobs that kick off in the middle of the night- jobs which can cause the CPU to spike in use and generate heat.

A better bet is to just keep the fan on a constant, but lower speed using fan control software. Say around 1500-2000 rpm.

That plus an SSD should allow you to have manageable sound levels, while retaining the performance of a full MacBook Pro, as opposed to the less powerful fanless MacBook or MacBook Air.

For the near term verification need, I'd recommend:


going to a local electronics store with a minimum 14 day return policy (Amazon would also work), purchasing an SSD drive and a hard drive enclosure
Then install the SSD drive in your computer and the old hard drive in the external enclosure
Then manually install Mac OS X to the new SSD and, using the external enclosure, restore your data to the new SSD drive from the old hard drive.
monitor the sounds levels over a week or so to see if they've improved.
If not, then you can swap the hard drives and use the external enclosure as a means to allow you to wipe the new SSD. Then you can return both of them to the store. 


If you really want to risk your system's stability and potentially cause damage, you cannot use Mac OS X, as Apple has it locked down to prevent turning off the fans. 

If you can dual boot with Windows or Linux with boot camp you can use the app called "speedfan" in Windows or a terminal command in Linux, "pwmconfig".  Both of those might allow you to turn off the fans completely, but at a risk of system damage.