From your question, I gather that there are a couple issues on the table for you.
You would like your child to be in the optimal learning environment for him, and you express some frustration with the school system itself for the way the environments are structured and the way certain services are delivered.  You have a lot on your plate to address.  

Let's take the issue of a scribe first.

Being interested in your son's having an assistant to scribe for him seems to be an appropriate concern.  You did not say what state you are in; and it is important to note that the way special services are delivered may vary from state to state.  However, I am assuming that since your child is in a self-contained classroom, that he has an IEP within your school district's special services department. If this is correct, then the IEP meeting would be an appropriate place to begin the process of obtaining the scribe.  

My suggestion is that you speak to your child's teacher (or the director of your special services or special education department) about calling an IEP meeting where a determination can be made regarding the service you want your son to have. It is my understanding that a parent's request can initiate an IEP meeting. In addition, you might want to do some research about the use of scribes to present as back up information for your request if you deem it appropriate.

If the IEP team determines that a scribe is not warranted in your son's case, you might choose to discuss what modifications can be made for him to help him with his fine motor issues, and his writing.  For your high functioning, intelligent son, a case could be made that he would be well served by services that promote his resilience and independence with writing by offering him fine motor strategies. You did not say whether he was receiving OT services.  If your school system offers OT, an IEP meeting might also consider determining that he receive those services instead of, or in addition to, a scribe.

Now, for your perception that it only behaviorally challenged children who have assistants.  This might be an issue to raise with your special services director.  He or she might help you understand the protocols by which assistants are assigned. In this way you may gain a clearer picture of how these services are delivered and to whom. Hopefully such a discussion might help you feel more comfortable with the system itself.

The most important piece of advice I can give you is to encourage you to be an empowered parent.  Ask questions, make requests, gather information, and follow the protocols your school system allows for advocating for what you deem to be in the best interest of your child.  You may not be able to control every outcome, but you can become a powerful and appropriate advocate for your son's education and welfare.  

Bette J. Freedson, LICSW, LCSW, CGP