How do I deal with an old reference letter from an advisor for job applications?
Not exactly an answer, but a couple things to note.

Letters on MathJobs expire eventually; I think you can see the expiration date on the "cover sheet" page. It will be very awkward if it expires partway through the application process. 

Also, note that your advisor will be able to remove or update the letter at any time, which could be a problem if he is really vindictive - he could replace the letter with something unfavorable. 

So in short, regardless of how an old letter looks to the committee, it may not be wise to use the letter against your advisor's wishes.