I think this is a great start actually. That "yes", which acknowledges what the other person just said, is way more important than you think.
Think about it in terms of being objective, rather than small talk/being fake. If you had a report with good & bad statistics, or referencing pros & cons, you wouldn't just mention the bad statistics or the cons in the report's final version. That would be incomplete or misleading.
Likewise, always acknowledge the value of what the other person is saying first, whether you go on to agree or disagree. You can memorise some stock phrases, like "that's good to know", "true", "thanks", "I see where you're coming from", etc.
This actually isn't just an ASD thing (though yes, I know it may be harder for those with ASD)! At work or in their personal lives, a great deal of people might hear something and agree with/compliment it in their head, then jump to the bad part aloud: "But [objection]..." This gives the impression that they disagree with it more than they actually do, and causes a lot of friction in daily communication. My tip is to "state the obvious" by first stating that you do agree with certain parts / think it's a good suggestion / etc.
As a more advanced step you can also learn to restate what they're saying to reflect you've heard it and value it, but honestly even a lot of NT people don't do that.