See this page for details on forcing SSL:
http://www.besthostratings.com/articles/force-ssl-htaccess.html
SSL should not have an effect on your SEO URLS if it is implemented properly.
with the google libraries, they do support SSL. all you need to do is remove the protocol from the link, for example, instead of:
<script type="text/javascript"
src="http://ajax.googleapis.com/ajax/libs/jquery/1.2.6/jquery.min.js">
</script>
use:
<script type="text/javascript"
src="//ajax.googleapis.com/ajax/libs/jquery/1.2.6/jquery.min.js">
</script>
this will cause the link to automatically detect whether to request the script using https or http based on the protocol used by the client.