We've had issues before with links that include the mkt_token but when I'm using the skeleton template for emails, I don't see how to remove it via UI. Is there a way to remove mkt_token but we still want to track the link.
There are ways to do anything you're trying to do. But, what "issues" have you seen? We don't recommend removing the mkt_tok from your links unless there is good reason. This is what enables Marketo's munchkin tracking to identify the lead and associate anonymous activity correctly.
In one of our emails, we included the mkt_tok and when a user clicks on it, it loads a page of code instead of the actual page. And this has happened several times.
What are the ways to remove the token from the template?
If having mkt_tok appended to your links creates a problem, that's something that can (and should!) be fixed on your webserver. An example of a potential problem is here: http://blog.teknkl.com/big-brands-bad-code/. In this case, the webserver had a broken notion of what was and wasn't allowed in a standard URL. Some testing by your devs should show them what they're doing wrong -- it might even be exactly what's in my blog post, so you they should check that out.
Like Justin said, turning off mkt_tok with no other way to associate leads kills fundamental functionality of Marketo. It can't be better to live without tracking than to work out the probs and fix them (they're never that hard!).
It can be done on any <a> tag and you can edit the Marketo Starter Templates to have that class for links. You'll also see that in the rich-text editor, users have the ability to uncheck "include mkt_tok" when they add a link through the rich text editor for a text element in the email.