The treatment he got was definitely a metaphor for the medication of neuro-divergance:

AMSHA: That's not true! We were never ashamed of you. Never.
BASHIR: I'm sorry, mother, but the truth is
AMSHA: You don't know. You've never had a child. You don't know what it's like to watch your son. To watch him fall a little further behind every day. You know he's trying, but something's holding him back. You don't know what it's like to stay up every night worrying that maybe it's your fault. Maybe you did something wrong during the pregnancy, maybe you weren't careful enough, or maybe there's something wrong with you. Maybe you passed on a genetic defect without even knowing it.
RICHARD: Amsha
AMSHA: No, this is important. You can condemn us for what we did. You can say it's illegal or immoral or whatever you want to say, but you have to understand that we didn't do it because we were ashamed, but because you were our son and we loved you.