It would be nice if it wasn't an issue. It is what we make it and it can be important to look nice or look sharp. The older we get, we have more of a 'do what we want' attitude and also depends on your self-esteem (not caring what others think) and depends on your values. As a kid though there are some pressures for some to want to fit in or blend in, and not get picked on; some kids will not notice and not care but others will hone in on the differences specifically to use them as a reason for teasing and bullying. This where the concern comes in for younger ones, trying to prevent this and wanting to be like the others so as to not stand out. Building up their self confidence and their esteem for their individuality is important to be themselves no matter what happens or in what they do, how they carry themselves in any circumstance, and for what they make of it. If they like it, it's what matters; it can be cool as long as they are comfortable, wear it with style and confidence. It's not what other's think, except to follow the rules of the school for dress, and from there be themselves.
In all, the pants themselves are not an issue, it's fitting in that is that is probably the concern. Yes, the pants are a better choice than the PJ's, only he will know they are women's as long as he does not tell (if fitting in is the underlying concern.) I'm sure the pants will go over just fine. You are very supportive and a kind sister to be there for him. I'll thank you for him.