Forgetting everything about missiles and keeping under the government radar, I'd say a more practical and compelling argument against active control is cost and weight. Model rocketry goes up to G motor class, and even a G motor can't lift all that much weight. And for an active guidance system, you'd need a contoller (you might be able to do it with an Arduino, but I don't know if it has the computing power to do the job), sensors and the active control system. That all adds up, and only adds to the weight of the rocket and motor. Not really feasible in anything that isn't a decent sized high power rocket (it's an "ecomomy of scale" thing).
Second is cost - all that extra hardware is going to add enormously to an already very expensive high power rocket, when passive control (ie fins) works just fine and doesn't add anything to the costs.
Third, you need to consider that none of the hardware and software is "out of the box". That means designing the system, putting it together from scratch and doing the programming yourself. And I can pretty much guarantee that it won't work the first time out of the box, and while a passive control failure can be spectacular (skywriting, land shacking and lawn darts with an H or higher can be really scary), an active control system failure would be just as bad and pretty much a given. And, harking back to point 2, each failure is likely to destroy your hardware completely, so that just adds to the cost.
Finally, there is the time factor. You could spend years developing such a system with only a handfull of launches. Meanwhile those of us flying standard passively controlled rockets have probably gotten in hundreds of flights, all still exciting and fun.
And it isn't like the state of rocketry hasn't progressed since its inception - there have been lots of developments since or hobby's pioneers launched and recovered their first 3FN model - we have boost gliders, rocket gliders, rcrg, helicopter, superrocs and electronic payloads, just to name a few. And as far as the big boys go, electronics development has given us smaller and more practical dual deploy altimeters, live streaming video and gps tracking systems. Active control HAS been tried (I believe there was a NAR R&D project on this and I remember reading an article written for the NAR magazine about that project) - it just is too expensive and time consuming to be practical.
Me? I'm perfectly happy launching six or eight low power flights at any give launch at only a few dollars per flight. But that is what works for me, and if you want to experiment with active control, go right ahead. The key to any hobby is doing what makes you happy and keeps you interested.