I’m not entirely clear on what you’re trying to do, but I assume that your ‘bookmarks’ are named anchors in the page itself? And that including those anchor names in hash tags in the URL causes the browser to jump directly to the named anchor on the page rather than starting at the top and smoothly scrolling down? I don’t think you can stop this behavior. You can see an example of what I’m thinking you’re doing here. Notice that if you load the page with #two in the URL the browser jumps to section two without scrolling.
You’ll have to use hash locations that don’t match anything on the page directly but can be processed by your script to find the correct location on the page and scroll to it after page load. That way the browser will do nothing because it can’t find the anchor, but your script can. So in the above example you’d have a named anchor on the page named __two or something similar, then if you load http://server/#two your script reads location.hash and scrolls down after munging the anchor data.