Do you store your API keys and other sensitive data with a site that doesn't even have a page discussing their encryption or security practices? Their privacy policy mentions they secure data with SSL protocol...

Who has access to each client's database? Is it audited? Is it encrypted at rest? I'm sure it is, but Config.ly would be wise to add this information to avoid fears.

Also you can store encrypted secrets in Git just fine, there are a number of methods to do so very safely.