I'm sure you've done work in an organisation that wants to exert its control over users, one of the common things that I've seen is the disabling of menu items like the 'delete this web site' option.
The last thing you want to do is edit the pages on the file system, this will just cause issues when you apply a service pack or if you bring a new WFE online because each server will need the same hack.
Instead you should build a solution that makes use of the HideCustomAction definition.
For the above delete site link, the Elements.xml file should look like:
<?xml version="1.0" encoding="utf-8" ?>
<Elements xmlns="http://schemas.microsoft.com/sharepoint/">
<HideCustomAction Location="Microsoft.SharePoint.SiteSettings"
GroupId="SiteAdministration" HideActionId="DeleteWeb"
Id="HideDeleteWeb" />
</Elements>
From here it's just a matter of referencing the above elements.xml in your feature.xml file and building the solution in the normal way.
To find out what the ActionId, GroupId and Location you can refer to this MSDN page.
Now you can safely change the menu items, but be aware that the files still exist on the file system, so in the example above if a user still knew the location of the delete web page they could still delete their site.