Hi Cricketer,
As long as the metered number is not in your source code, then you will be OK.
The proper way to use trackable (metered) phone numbers to track phone calls from organic searches, is to use javascript to re-write the original phone number in the visitor's browser with the metered number, but only when a visitor's referral string contains a url from the search engine you wish to track.
Your metered number service should be able to provide this javascript code block for you. It's typically less code than the GA script.
We've been doing this for many years, and have never had a problem.
The only time I see issues, is when an IYP (internet yellow page) site, uses a metered number directly in their listing for your business. Although it's nice for their own tracking, I've always found that search engines like to see consistency in business listings across the net. In these cases, I ask the IYP to set the business's phone number in the listing back to the business's non-metered number.
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I know a company that> provides a javascript code block to all clients which accomplishes the rewrites for each website. There are many other company's in this space that do the same thing.
Hopefully that helps.
-JB
[edited by: aakk9999 at 1:44 pm (utc) on Feb 3, 2014]
[edit reason] Removed specifics [/edit]