I went through this process with Litmus and was able to add its code to the HTML email template in Marketo's template section (under the Design tab). I remember there were some minor problems, but overall the code worked fine. If I remember correctly, the only Litmus option that was unavailable as a result was ability to track forwards and printing, or something minor to that extent.
I've raised this issue with Marketo on several occasions - please allow to turn off your wysiwyg on a per-user basis. They are completely uncooperative, stubborn, oblivious, and deaf to these requests. They believe they know better by forcing their wysiwyg to those who don't want it.
On the other hand, Litmus support was absolutely fantastic in helping with this issue.
Good luck!