I agree and disagree
About the stock kits being able to take the larger motors. IMHO, if you build well using normal techniques (fins are straight, you add fillets, etc) most Estes 3/4FNC rockets will handle one step of motor upgrade. That is a C powered rocket will handle the AT D21, and a D powered rocket will handle an E15. I said 'most' because I am not that familiar with the current fleet. Note also I said 3/4FNC, some of the exotics with odd and large wings may not handle it. Examples that work well with E's are the Big Daddy and Mean Machine.
Where I agree, is that the composite engines will deteriorate an Estes rocket quickly. Oddly, in my experience, it is not due to the higher thrust, but due to a more enerjetic ejection charge, and that the delay grains burn after the ejection charge has fired. A small diameter rocket, BT-50 and smaller, runs the risk of structural problems due to charring. I had an original Sizzler that was Bt-50 based and after one flight on the D21 the rocket body was bubbled (the tube not the paint). Some people add liner tubes and the like to avoid this problem. The other thing is the elastic chock cord doesn't hold up to well with composites. A short piece of Kevlar twine as a leader fixes this problem.
BTW, eugene, this was an important point to bring up, rather than just my original short answer. Good input, man. Unfortunately, the length of my answers are often proportional to haow busy I am at that moment.