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You can take the web.config file from a Blank Project. If you do not have a Sitefinity Blank Project you can download it from your Client.Net account. Just in case back up your database. Then add the web.config to the project. By default you will go through cmsstartup but it will only ask you to make the connection to database, and perform a check for existing administrators.
You can also avoid going through the cms startup by disabling it in the web.config. However this means that you will need to set the connection to your database manualy through the web.config file. To disable the startup, you can modify the following line in the web.config:
|<cms defaultProvider="Sitefinity" pageExtension=".aspx" disabled="false"
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