The observation that the level of knowledge, skills and achievements shown by someone finishing their PhD varies wildly both among institutions and also among students at the same institution is a very widely made one, but nevertheless is still striking to those who observe it for themselves. At my current institution, we have some graduates that I really wonder how they could possibly have gotten through the program, and we have other graduates whose superior work shocked me: once every few years a graduating student in my current department (UGA math: about the 50th best in the country) has a thesis that would have been regarded as distinctly strong at the department where I received my PhD (Harvard math: always in the top three). Is the variation lesser at a place like Harvard? No, I think it's greater. In 2003 I graduated from that department with a respectable thesis. One of the 2004 graduates had a thesis that was, suffice it to say, orders of magnitude better. Do Harvard math PhDs have an understanding of the relevant mathematical processes? On average, yes, to a reasonable degree. All of the time? No, probably not.
I don't think it is helpful to cast the problem in "whistle-blowing" terms. That suggests some kind of clandestine nefarious activity, but so far as I know most interested parties are acutely aware of the issues raised by the OP and described above. If the OP is a tenure-track faculty member at the institution he describes, it is (to say the least) entirely his right to take action to enforce higher standards in the PhD program. I don't understand the need to do so anonymously -- you don't need to do your job anonymously, and doing so sounds difficult.
Here are some thoughts about how to get involved with this.
1) Pace yourself.
The cliche is that young faculty members come in wanting to fix the new department. In my experience these desires are overall quite positive, but they need to be tempered with an awareness of how the department actually works (which will not be exactly the same way as the few departments they have previously been involved with) and also need to take time to get to know the personnel.
While you are an assistant professor you should start serving on thesis committees of other students. You should be conscientious but less vocal than you plan to be in the future: you have a lot to take in. In particular I think it's best if you spend at least a year observing PhD students and the PhD program before taking on students of your own. So long as faculty are invited to exams and thesis defenses, make a point of showing up, even if you are not on the committee. If such events are not typically open to faculty members, consider asking if you can show up "as an observer".
2) As long as you are confident that you will not be making real trouble for other students and faculty, don't be afraid to enforce your personal standards. You need not be held to the lowest common denominator.
As a faculty member in your department, some portion of the task of setting the standard for the students falls to you. You can be stricter or more exacting than some of your colleagues, so long as you are not making bitter enemies or ruining people's lives. In my department, the oral exams run by my research area are well known to be longer and more grueling than anyone else's oral exams. Maybe this dissuades a few people, but not too many since more students study in my research area than any other area. A faculty member who has a reputation for high standards and working with students to meet them often becomes very popular and influential in the department.
3) Realize that the thesis defense is too late to "hold the line" for any standard other than the requirements of the thesis work and the written thesis itself.
Academic traditions must differ a bit, but I have never seen a thesis committee test for basic knowledge during a thesis defense. The job of the thesis committee is to make sure that the thesis is an acceptable written document and of course to convince ourselves that the student was responsible for it. That is not a formality: it often involves hard work down to the wire by the student, the advisor and some of the committee members to get the thesis in acceptable shape. The thesis defense itself really is a formality: in my experience whatever issues may remain with the written thesis are not even much engaged at the defense itself, though they may still be dealt with later. If the committee doesn't think the student is ready to get a PhD, the thesis defense should not be scheduled. Period.
If a student exhibits a lack of basic knowledge at the thesis defense: yes, that's a distressing failure worth doing something about. But the failure took place years before. Most PhD programs have several rungs of exams, both written and oral, extending over several years. A student should not be able to pass these exams without a knowledge of the fundamentals of the field. Moreover the typical culture of academia is that not everyone passes these exams the first time they take them. Generally speaking it's quite culturally acceptable as a faculty member to say "Sorry, Student A doesn't know Subject X well enough to continue on with his studies." In my experience, these kind of exams are often done relatively quietly in the department. Some faculty -- maybe those who are directly affiliated with the most relevant coursework -- are involved in administering the exams. The majority of the faculty may not be. If you're crusading for higher standards (not a bad thing!!), this is your place to get involved, get active, and draw your lines in the sand. Take time to figure out exactly what the problem is. Are the exams not being graded seriously enough? Are the syllabi not testing what you want or not testing it to a high enough level? Are the advisors of students given an undue influence over the result of these exams? (E.g. "It is a waste of my Student A's time to know Subject X. I want him to work on Subject Y only.") Once you've identified the problem(s) you can get to work on the amelioration process, patiently but implacably. Because it is in fact not a criminal conspiracy, if you are passionate, smart and keep your eye on the ball over a period of years, you will have more of an influence than other faculty members who are a bit too lazy, too "nice" or too whatever to run things in the best way.