I don't understand the problem.
You need to call the menu two times.
First to get the menu entries.
Use smarty {capture} to assign the output to a var. (to avoid processing the menu for each content again):
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{capture assign="menu"}{menu ... }{/capture}
Second to get the content output.
There you place for each content the menu we just captured:
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{foreach from=$nodelist item=node}
<div id="{$node->alias}" class="scrollto_container">
<a name="{$node->alias}"></a>
<div class="menu">{$menu}</div>
<div class="content">
{eval var=$cgsimple->get_page_content($node->alias)}
</div>
</div>
{/foreach}
This will give you the content of all pages wrapped in a div with id="[pagealias]" and an anchor link named with the page content alias (to be able to use your site without js).
All you need to do now is to create a menu template that just links to that anchors:
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{foreach from=$nodelist item=node}
...
<a href="#{$node->alias}" class="scrollto">{$node->menutext}</a>
...
{/foreach}
If the anchorlinks still cause a reloading of the page you can prepend the root_url to the menulink:
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<a href="{root_url}#{$node->alias}" class="scrollto">{$node->menutext}</a>
Additionally you need a js that tells jQuery what to do if links of class "scrollto" are clicked but returns false:
I don't understand what this has to do with mod_rewrite.