The “just” there sounds polite to me. It apologetically implies that you realise the person probably knows about rsync already but maybe didn’t use it for some requirement not yet discussed, which you’re now asking about so you can give a better answer.
I think on its own the sentence is fine. However, in the cultural context of tech discussions on the Internet, "why don't you just [X]" is usually passive-aggressive or an indication the person asking this hasn't taken the time to consider the use-case or constraints, and might even insultingly belittle the person for not having considered such a "straightforward" "easy" solution.
I myself balk at the sentence all the time, and I have nearly stopped using it in any communication because it doesn't communicate the right thing.
Yep, there are multiple ways to interpret it, but that's the problem, particularly with written text. When spoken the word "just" and the tone of the rest of the sentence convey significant meaning that is lost when reading it.
