I think your question can be rephrased like this:
Should you do what you think it's right, or should you not, because it is likely to bite you back?
From my experience, nobody likes to be contradicted. Regardless of the context, or even the possible benefits that changing their minds can bring to them, people simply hate it to be contradicted. No matter whom (the journal, the authors, etc) you raise the issue, you'll be perceived as a pain in the ass, smaller or bigger, depending on how diplomatic you are.
What you need to do is to assess 2 things: what you lose and what you gain if you contradict someone. When assessing losses don't forget to include things like the spent effort (like posting this question here) and the virtual losses of debates which you may not have since the current loss will exclude you. When assessing gains don't forget to assess things like the societal impact.
In short: pick your battles. Only you can answer which are worth fighting for.
Edit: People keep misinterpreting my answer, which indicates that it is not clear enough. This is an attempt to clarify it.
Any answer that she should reply about the misuse of the pronoun or that she should let it go, is, in my opinion irresponsible. None of these 2 decisions can be reached simply by using the information provided in the answer. Such a decision should depend on many things, some of which are very personal details about the Original Poster (OP) (some examples are: is she currently involved in a lot of projects, is she currently over stressed, what is her relationship with the journal, does she care about it, can this affect her career, to what extent etc). Due to the nature of such details, I do not expect the OP to clarify the question, but to be helpful, I indicated a basic possible framework, which can help her reach a conclusion of her own.
Most people who already answered here believe she needs a push towards a decision, or a public poll on the matter. Her life is not a democracy, and her personal circumstances are not the same as other people circumstances. It is fair to say what one would do in her position, it is not fair to tell her what to do, from a selfish interest to promote the interests of the answering person, disregarding the possible detrimental effects on the OP and her agenda.
To exemplify, in her position, I would let it go, because I do not think that using the male pronoun as a neutral gender pronoun means anything more than that. I do not think it is non-inclusive, but a mere artifact of how English evolved over thousands of years. Even if it might have had non-inclusive origins (a fact that I do not know of) thousands of years ago, it does not have a non-inclusive meaning now. Still, I personally use they when the gender is not clear, because I know it might bother other people, and whether they are right or wrong, I still don't want to annoy them or disrupt the flow of whatever we were doing.
Even if in OP's position, I would let it go, I do not think that this is the best decision for her to take, because the optimal solution depends on her circumstances, of which I am not, and I cannot be aware of. Simply said, I am not her, and I encourage you, the OP, to carefully look inwards for an answer.
I hope that with my edit, which in my opinion, is just rephrasing and exemplifying my original answer, the answer is more clear now.