That's a curious statement for a 2.5 year old to make. Have you, DH, other family or friends said something to that effect to DS? Like, in response to a question about why someone else is eating cheese/meat, has anyone said something like, "this is how we choose to eat now, you can decide how to eat when you're older?"
I have a friend who has explained food like that to her DD, mainly because mommy goes back and forth between vegetarian and vegan, while daddy is decidedly a meat-eater. So she has to kinda toe the line, she can't just say "this is the decision that was made that is right for our family," she has to allow room for multiple points of view. But, that has resulted in her DD trying foods that daddy was eating that my friend really really really didn't want her DD to eat, ever.
If you or others have said things like that, I'd stop, and instead just focus on what dietary choices your family makes. The end. Nothing about changes in the future. This is what we do with our DD, who will be 3 next month. She understands that other people eat meat, and she'll often list through the people she knows- grandma eats meat, cousin eats meat, friend doesn't eat meat, we don't eat meat. I think the reason she hasn't followed it through to the "but when I'm older I can make my own decisions" point is because no one has done or said anything to her to suggest that there would be a reason to re-evaluate that decision at any point. Basically, it is what it is.
To your main question- when to let kids make their own food choices- I don't have an exact answer, but I will say, not now. Not at 2.5. He's too young to understand health issues, ethical issues, financial issues, environmental issues, etc- all the things that influence our choices we make for our families food sources. So, I guess, whenever a child can begin to discuss and understand these issues- then I would consider letting the child make his/her own decisions.
But one last thing, which might seem to contradict what I just said- I don't freak out if DD has something I would not want her to have when she is not in my presence. Meaning, if I am with her at a party, and she sees and asks for Jello, I say no, that has animals in it and we don't eat animals. And that's the end of that. But when she came home from daycare and said that she had Jello, I didn't freak out, at her or the daycare people. I just said "oh, that's nice" to her and made a mental note to tell the daycare that the whole "no animals" thing includes seemingly benign products as Jello and certain fruit snacks.