I'm not sure if the issue is to do with the latest 10.4.4 upgrade or something specific (ie. gone wrong) on your computer or how some websites are implementing password entry.
All I can suggest at the moment if its the former is to remove the password that's saved for the troublesome site(s) by going to Safari Preferences Password tab, enter your login password then search for the site, select and then click "Remove". That way it can't autofill which might give you time to do the other entries (but make a note of the details first and keep safe).
Unfortunately you can't disable Autofill per site, only globally by unticking the box in the top left which if the majority of sites are fine can be a bit of a pain, filling one or two sites in by hand is one thing, having to do it for all might not be such a good idea.
I believe the issue may be a combination of Apple changing something in the last update coupled with how web sites implement password entry, the reason I say that is when visiting an Apple site I get a box for ID which I can click on a suggestion to fill, then a second dropdown box appears which I again get offered a suggestion to fill password, only then will the site open.
Another site does roughly the same but after the ID entry part it goes to another page for the password entry, but still with the suggestions popping up as before.
A third site I tried was similar to Apple's but once the suggested ID was entered in auto filled password and jumped straight to the page, strangely this one prompted me to "save new info", on further investigation the password had been change to a very long string of characters which it was trying to re-save, this had to be declined for obvious reasons.
So, until either Apple gets around to sorting this or the "troublesome" websites update their login pages I don't see what else you/or I can do.
Hope some of this helps.