Q: My student can do R in all words and in all positions, but he prolongs it. Do I need to teach him NOT to do this?

I would teach it to him if it did not go away by itself within a reasonable period of time.  I am not sure what that reasonable period of time is, but I would be willing to give him 6 months to a year to straighten this out.

I probably would give him a few lessons on this and then let him go with periodic checks every few months.  Use negative practice in these lessons, and have him compare long and short productions.  Make a long one, and then a one short, and go back and forth between the two.  This is ear training.  Teach him a simple rule, “We make R short like all other sounds.”