What is the procedure of testing something with the tube without the wild harmonics and peaks the gating is generating?

1. It is not recommended at all, but if you want to do so, then:
Go to the Control Tab, put the mouse over the generator number you want and click the right button. I'll appear a dialog asking you if that generator is always running Spooky2 Central. Click on "NO", and after that, you'll be able to change any parameter you want, because the built-in protection has been disabled.
After your testing, don't forget to reverse the process, answering "Yes" to the question, to re-enable the protection.
You can read about this on the User's Guide, page 57.

2. Gating is achieved by changing the amplitude to 0V and for that to happen a command needs to be sent from the PC to the XM generator.
My guess is that 66Hz is probably the upper limit as it is close to the Windows context-switching limit of ~15ms.
See accepted answer here:
http://stackoverflow.com/questions/12320748/how-often-per-second-does-windows-do-a-thread-switch
On top of this, Spooky2 was using windows timer for channel refresh rate so a gate above 10 Hz becomes problematic in my opinion.

As far as the protection goes, if you turn it off, be sure to keep the amplitude & waveform parameters the same if you change the gating.

For more details, please check the link from:
http://www.spooky2.com/forums/viewtopic.php?f=74&t=6808