Very similar to in WSS v2, in WSS v3 the project element within the
onet.xmlis still what controls this editting feature.

msdn2.microsoft.com/en-us/library/ms438080.aspx

So much like in v2 of the platform, in your onet.xml you include:

DisableWebDesignFeatures="wdfopensite"

Is there any way can we block site editing excluding few super
admin?

Sure, don't give them SharePoint Designer.

In Central Admin > Application Management > User Permissions for Web
Application, under Site Permissions, there is a checkbox for Add and
Customize Pages. We have been under the understanding that deselecting
that option would limit people's ability to edit or custom code pages
using FrontPage, Designer, etc. It seems to be associated to the option
above it, Manage Web Site (if you deselect the former, it also deselects
the latter, which we do not want). However, I've been told that all
performing this action would do would be to limit the permissions that
can be given by the site collection admin, not the action itself. I've
tested with FrontPage and have not been successful at opening MOSS pages
in FrontPage 2003 for editing. I do not have Designer yet, and would be
very interested to hear from anyone who has tested this, as we want to
prevent our site admins from customizing sites/pages in this way.

Removing a permission level from a Web Application should limit that
permission level in any site within that Web Application.

You can also create/add a Web Application policy and restrict SharePoint
Designer/SOAP on <All Zones> or a specific zone. Default is the
'default' zone for every Web Application.