Stick to your guns, you are right.
Your DS1 is your eldest so you haven't had chance to experience the fact that they do just grow out of it when they are ready. They really do, and you may as well bang your head on a brick wall as try to "discipline" a child out of separation anxiety.
As your son gets towards three or three and a bit, you will see the anxiety reduces and is gradually replaced by an interest in exploring the world and making friends. Of course it ebbs and flows, especially when they are ill they can still be clingy even as older children. But the general trend after three is for them to be more confident about separating, its like a new drive to get out there into the world a bit takes precedence over the anxiety.
Your in laws are making a massive assumption about your DS's maturity, essentially they are assuming that his understanding and perception of the world is the same as theirs and they are having a major failure of mentalising abilities if they think your DS is trying to manipulate you.
In order to manipulate, you have to have got to the stage where you understand that other people have separate minds to you and that you can use that to your advantage.
See the mentalisation test on you tube or get your son to do it; it will clearly show how (age appropriately) immature your son is in terms of his sophistication of understanding.
Basically, you get a teddy and two pots and a coin. Let teddy see you hid a coin under pot A. Then take teddy out of the room, leave teddy outside, and come back in, and say to DS that you are going to move the coin to under pot B and that it is a secret. Then bring teddy back in and ask your DS where teddy will look for the coin. Your DS will say that teddy will look for the coin under the second pot, BECAUSE THAT IS WHERE HE, DS, WOULD LOOK. He is not old enough yet to realise that teddy's experience and knowledge is different to his. How on earth a child of this immaturity can be thought "manipulative", is beyond me. Your son will probably be well on the way to four years old before he can get this test "right".
At 2.5 your son is still wrestling with object permanence, i.e. whether things continue to exist even when he can't see them. He is just about clocking that they do.
The world must be a confusing place for tinies. The last thing they need is discipline around these kinds of issues. Of course they need boundaries around bad behaviour like hitting, screaming, snatching, chucking food. But not around something like separation anxiety!
Enjoy him and follow your instincts. When he is older you will be able to look back with the bigger picture of how little he still is.