There are a couple of different issues mixed together in your post. It might help you to separate them in your mind.
Blaming the teacher for not coming out to your son won't help you or him. You don't know what was happening in the classroom at that particular moment; she may have been unable to excuse herself (even with an aide there). She also might have felt that "If I go out there it might upset him even more; he might see that as the big bad teacher dragging him into class; he will feel singled out if I march him in here, late, in front of everyone else." And so on. In other words -- Try to step back a little from your anger and upset, and consider that maybe she was trying not to make things worse for your son, especially if she knows that he is a bit intimidated by her already.
Separate issue: You said that your son is "very shy and quiet" then said that "he has friend and is never alone." A shy kid certainly can have lots of friends, but the fact the teacher says she's concerned about him "socially" is something you might want to take more seriously. She sees him for most of the day, interacting with his peers, in situations in which you do not get to see him. Yes, you know him better than anyone does, but one thing you will find as he goes on in school is that our kids can be quite different people in school than they are for us at home. When she says she is concerned "socially" she may not mean "He doesn't have friends," which seems to be how you're reading it. She may mean that he has issues with how he deals with other kids, or is very easily upset by things that don't upset most other kids, or he doesn't move easily from one activity to another--anything. You can't know until you ask her, and be open to hearing her definition of what she means.
If he hates getting into trouble, he may well be a perfectionist kid. That has benefits and drawbacks, and in first grade, largely drawbacks, as these kids (mine is one of them!) want to please, please, please the teachers and are shocked and upset when they don't do that every time. It's good to want to please the adults but it also causes them so much pain when they're not perfect -- as you saw when he had such an extreme reaction to having one smiley taken away. He's at an age when adults need to guide kids on how they react to adversity and to being imperfect. The teacher and counselor can help you with that if you let them.
When you talk with the teacher, see if you can focus on the bigger picture instead of your concern about why she didn't come to the door in that one moment. I would ask her if the school counselor could meet with your son (after meeting first with you alone, or with you and the teacher). This is what counselors are trained to do -- help kids over these humps when they are having troubles. I've seen it help kids a lot just to have a few weeks of meetings to play games and chat with the counselor, so that may be a route to try.
One other thing. Next time he's anxious and doesn't want to go to school, be prepared in advance with what you will say and do to get him into school swiftly and without a lot of discussion or negotiation. He may feel that he now has the backup plan of "I can stay home" and will be prepared to try to negotiate that next time, but reassuring him, combined with a very swift dropoff and your immediate departure, probably would be best. You do want him to feel good about going to school, but when he doesn't, you don't want to stay in the school more than a moment or he will get more and more wound up; if you leave quickly but firmly he will have to go inside and get engaged.