It depends on how much rot is there. If it is just a small ammount, then yes you can drill the hole with a larger drill bit, plug it with a wood dowl, grind the glass to a V shape and reglass. You just have to make sure you get all of the rot. Its not the best way to do it, but it work. If its larger then a inch and a half you might as well replace the stringer. (or replace as above and use a rail kit for mounting)
the boat is ployester... you can use epoxy if you like, but I don't see the need.