Oh My! There are so many things wrong with this....It's really hard to answer without knowing more of his IEP and spec. ed. at the school, or even what the behavior was that caused the teacher to have him not return to the classroom.
Has your son had a Functional Behavioral Assessment (FBA) done? Is their a Behavioral Intervention Plan (BIP) in place? (this BIP addresses behaviors that your son may have and how the staff is to address them) You should have been informed immediately of his removal from class and why this was done.
An ARD can be called to meet to determine if this behavior was a "manifestation of his disability" and not just usual "bad" behavior. This determination means your child cannot be "punished" according to the student code of conduct for a behavior that is a manifestation of his disability, except for special circumstances (see below).
Yes, his rights are being violated--he is missing out on education time by being sent to a class by himself, as well as being singled out/isolated, if he has a BIP in place in his IEP--was it followed, does it need revision. But again, you need to know just what the behavior was as under IDEA a child can be removed from the class to an alternative placement for up to 45 days regardless of the findings of the determination of manifestation, if the child had/possessed a weapon, caused bodily harm to an other etc.
I suggest you go to the website www.wrightslaw.com and search for Behavior. This site is awesome and a must be bookmarked site for any parent/student receiving spec. ed. under IDEA, 504, etc. Another site is www.idea.ed.gov--again search behavior. Hope this helps some. Good Luck! ~DLA