After three years in the workforce, I am planning on returning to school to get my PhD. I currently have a master's degree. Recently, however, there has arisen a complication: my thesis advisor for my master's degree was just discovered to have been embezzling from grant money (double dipping using a fake employee) that was shared between him and two other professors (one at his own institution, one at another institution). His fraud occurred after I was gone from the university.
Because he was caught embezzling grant money, the entire grant was revoked and the other two professors lost their portions of the money. This represents at least two more years of planned funding that they have now lost through no fault of their own. The professor at the other university (call it University X) was one of my strongest choices for potential advisors if I was accepted to the program at U of X. She likely would recognize my name if I applied to the program at U of X. Because I do not know how she would react to an application from a former student of the professor that just caused her to lose a large grant, I am now hesitant to apply to U of X.
Even if I decide not to apply to U of X, I worry that admissions committees will see my former advisor's name and will black list me. My advisor was at least somewhat well known in the field (22 years of work in the field) and the number of people that are aware of him may be somewhat large.
I would just avoid mentioning my advisor's name if it was not for the fact that I published two papers with him. If I want to entirely cleanse my application of my advisor, I will also have to avoid any mention of these two publications. Not being able to include these publications in my application would obviously weaken my application. My advisor has a rather unique name (not just John Jones or something) and anyone who knows of the situation would immediately be able to connect him to what happened.
Will I still be able to get into PhD programs? Should I attempt to address my advisor's actions in my application? If so, how should I go about doing so?