The problem you're describing is probably more common than we think. But the way to go is not to disable SSL on Cloudflare, but to make sure you redirect to the proper version.
You have www and non-www version of your site.
You have http and https version of your site.
That's a total of four possibilities for URLs, and you should pick one and redirect the others.
There's no way around that. It's common practice and something every webmaster should do when launching a new website.
And you should also have four Google Webmaster Tools websites added, for all four versions, and only one will be active.
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