Maybe the site/doc you're referring to is marked as obsolete, but the technology behind is not. Here are the official links, not marked as obsolete:

• DpapiProtectedConfigurationProvider Class (with an example), there is also the RsaProtectedConfigurationProvider that is capable of encrypting sections
• Encrypting Configuration Information Using Protected Configuration
• Encrypting and Decrypting Configuration Sections
• ASP.NET IIS Registration Tool (Aspnet_regiis.exe) with the -pe option

I would definitely use this technology.