What is the standard way to include math equations in a CS research paper?
If you can write in latex, you should write on it versus word. The latex is specially designed to work with technical documents with a lot of mathematical equations.
Also, you can write math equations in word using built-in equation editor of Microsoft word or MathType as a better alternative than built-in ones. See this link for word equation for equation writing in Word with better configuration.
Technically the MathType produces equations with higher equality than Word built-in and I recommend it to use as a macro on Word.
About writing in Latex and then revert to Word, it wouldn't be recommended and will be reduced the quality of equations (due to reversion complexities and equation editors' of Word difficulties).
[EDIT: this answer refers to contexts in which the publisher is responsible for the typesetting. In contexts in which the author is supposed to produce directly a "ready-to-upload" pdf file, what I write is inappropriate, as correctly noted in the comments.]
Your only responsibility is making sure the equations are readable and understandable to the referees. I assume that the equations looked better in the manuscript that you first submitted, so you are clear.
It's the typesetters'/copy editors' job to make sure that the final pdf looks good, and they should be professionals who know the functioning of the software tools they use and the basic things to check when they convert from one format to another. They should have caught this problem before the paper went online, and fixed it themselves or asked you for a copy of the equations in a different format. They completely failed at doing their job.
You should complain with the publisher and request a change. In addition, you should also let the scientific board of the conference know informally, possibly by contacting the editor you have interacted with. The panel deserves to know that the publisher they use did such a bad job, because they are the ones that can complain at a higher level and change things.