I'm thinking that if I had roughened the inside of the marker body it could have held.
What?!
YOU forgot to roughen up the inside before casting epoxy?
That was the original plan, but the smallest practical tubing I had available was fractionally bigger than the marker interior so I went for this option.
Well, besides looking for small diameter pipe, you could also have looked for metal markers or pens. Or maybe some other kind of tube-like stuff some examples: hull of a laser pen, mini flashlight or maybe a bullet casing. Basically anything thats metal, cylindrical, hollow and on the right size should do the job better then a syringe tube.
You can also reinforce the plugs by making small holes and put bolts (or on this size, needles) through the pipe wall. Maybe denting/bulging the metal inwards would also do it.