When contributing to upstream projects (in this case non-MediaWiki projects), using the mediawiki.org address also helps to make clearer the contributions of the Wikimedia orgs as such. You ave probably found yourselves in the situation of finding that some redhat.com, hp.com or whatever.com/org dude is committing a patch in some upstream project, and how good that feels. It can't be bad to generate this type of impression to developers and contributors of open source projects out there.
For my part, though I consistently use my @member.fsf.org address, I generally include some mention in either the commit message(s) or some communication with the community that I'm working as an employee of the WMF. I've made inroads with communities that way, and it appears to be sufficient.
That too, and we have now this situation with the metrics reports. We get many times the question of WMF contributions compared to independents / 3rd parties and as it is now this is very difficult to calculate.
Can I suggest asking HR for a CSV of employee names, to which you should be able to easily add their email addresses (probably from the commit logs)? It might take some time, but it's also relatively simple to watch wikitech-l for new employee announcements and add them to the list. Checking the CSV as part of your metrics script would then be pretty simple.
Like Quim, I don't intend to force policy here, I'm just trying to solve the problems raised :)
(can we get some community insight, here, maybe?)