It looks like you can set the default top sites by editing a plist file for Safari.
The article that describes this process is here.
Even though this article mentions the beta, it should hold true for the release version of Safari 4 as well.
It seems that Safari resets this file when you perform the reset. To get around this, you can lock the file, which should prevent Safari from writing over it.
I reset my top sites using the reset command after locking my top sites, and they stayed the same.
To lock a file, get the file info (Command + I) or File -> Get Info. In the pop up window, place a tick in "Locked" and then close the Window.
This, combined with manually editing the file to get what you want on there, should stop Safari from Mucking around with your top sites.
There's more than one way to skin the proverbial cat.
From a terminal, issue the following commands:
sudo chflags -R nouchg TopSites.plist
sudo chmod 444 TopSites.plist
chflag nouchg removes the "user immutable" flag. I'm not entirely sure what user immutable means in this particular context, but I would say that it means we're not able to modify that file without being root.
Once it's had the flag removed, we can then chmod the file to 444 - which is completely read only. That should prevent Safari from making changes to it.