This is from the NIH guidelines for their visiting fellows. Opinions may differ, of course.
"Once you submit a waiver application to the DOS, please note that you have initiated a waiver, whether or not you follow through to complete the process. Requesting a waiver is incompatible with the J-1 exchange visitor program goal of returning home. Therefore, you may not be successful in applying for any further J-1 visas abroad or be re-admitted to the United States in J-1 status. You must be aware that if you leave the U.S. in these circumstances, you do so at your own risk."
Emphasis in boldface is my own.
In the experience of many of my colleagues, they had no problems reentering the US, but we have separately been told of others being denied entry because of their J-1 waiver application. So the above is correct: travel at your own risk.