You don't need to add the class manually in the code anymore, there is a checkbox in the "Insert Link" dialog that says "Include mkt_tok". Just uncheck it.
I disagree slightly in that this can be a permanent solution for files that you're directly linking to. If there is no landing page being reached with munchkin on it, then the mkt_tok is 100% useless.
Well, I suggest it as a permanent solution since inclusion of the string is the default state, not because the token is useful when navigating there. In most cases that I've seen this behavior, it will apply equally to both files and pages, as well, so doing this would resolve potential issues about the token system-wide.