Relations between China and the Philippines have been strained since the fourth quarter of 2007 and are now at an all-time low.
China recently executed several Filipinos charged with drug smuggling and, according to Filipino news coverage of the event, the Philippines had evidence that at least some of the people who were taken into custody and eventually executed were innocent of all charges (by the way, China executes more people per year than all other countries combined
according to a recent article in the New York Times
The chances are great that your employer is just trying to discourage you from bringing your wife into the country. Officially, Filipinos are personae non gratae in mainland China (on the immigration blacklist). While I never had any trouble renewing my Filipino wife's residency permit along with mine, we were unable to find a way of keeping my sister-in-law in the country beyond her original tourist visa and two extensions, i.e., for a total of three months. Whenever my wife traveled to and from Hong Kong and Guangzhou without me, she would be always be hassled when coming back into Guangzhou. Chinese Custom officials would completely empty out her pocketbook and start going through everything. It was very difficult for her emotionally.
There is no need to contact your embassy. If your wife has been in China before with a tourist visa, then you need to process her marital Z-visa at the Chinese embassy in the Philippines (Filipinos are only entitled to one tourist visa plus two extensions in their lifetime).
If she has never been to mainland China before, then you can bring her over on an L-visa (at least this was true a year ago). If you are going to process her marital Z-visa and residency permit in China, you will need an official translation of your marriage license (assuming you were not married in China or Hong Kong). You would simply take the official translated copy of the marriage license to your local PSB branch that handles residency permits along with her physical exam, passport, and photos. You pay a fee and they should insert a marital visa and residency permit inside her passport.
Your school officials should be helping you with this but I don’t think you actually need their help or approval.
Best of luck with this. Let us know what happens.