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.
Yes I have found the Litmus support to be fantastic. The response I got from them was:
"If you leave off the CSS, this will prevent the activity tracking for prints/forwards from coming through. You'll still see engagement and email client stats in your reports, however print/forwards will be omitted. As long as the tracking image itself is in the body of your email, then you'll receive the engagement/client data."
As a result of that information, I simply adding the img tag and left out the style information.
I am presently going through this issue right now, and I appreciate the feedback from both Gennadiy B and Samantha W.
It is unfortunate that the Marketo representative in this thread (Breno Gomes) provided feedback that was a criticism of the Litmus tracking code itself, rather than giving constructive feedback as to how one might approach this problem. His comment was completely unhelpful.