That should work. You can and should put the new Apache into a different directory (/usr/local/apache2 being the standard location). You'll need the --with-ssl=/path/to/your/ssl to get the SSL stuff to work, Then you can set up the Apache2 config file to point to your document root, use the old apachectl script to stop your old Apache, and then use the Apache2 apachectl to start Apache2. If something goes wrong, you can just switch back to your old Apache until you figure it out. One note, though, be sure to modify your init scripts to start the new Apache instead of the old one.
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