I want to deactivate my account from another ps3 from the website but it only gives the choice to deactivate them all and I don't want to wait 6 months to activate it again.
You don't have to wait 6 months to activate again. You have to wait 6 months to use the deactivate all feature again.
The web site can only deactivate all of the consoles on a PSN account. The only way to deactivate a specific console, is to do it on the console itself. Once you use the Deactivate All function, you can immediately activate two consoles of each platform under the account. You can also deactivate and activate consoles from the console itself as much as you want. As ne1atall stated, the only thing that you have to wait six months to do is to deactivate consoles on the web site again. You can always activate a console, if you have not reached the activation limit for your account.