I don't think they have the moral high ground because they do make a lot of mistakes with their proactive strikes.
The difference here is that this is obviously a confirmed Orchis terrorist cell and they are definitely building weapons to deploy against Krakoa. So it's a confirmed target.
However, you might be right in thinking that Hickman might continue the comparison to the American military in future comics and have the X-Men make some mistakes on some of the targets they go after, or show the X-Men getting bad intel that leads them to the wrong location. There are definite ways to show how morally grey proactive military engagement can be.