As Gray laid the groundwork for Sonnenschein, I would not call her a “fossil” by any means. Gray is not only one of the most influential university presidents in modern times, she goes down as one of the great ones at UChicago. It’s important not to view the College as the University. The College is one division that, at the time, happened to be under-utilized. I would predict that Gray was 100% on board with the changes that Sonnenschein wanted to make; her appointment of Boyer right before she retired spoke volumes, as it turns out. Gray has been one of the most vocal proponents for free expression at the university. As a renown scholar of history, she’s no slouch on the academic side either.
In short, Gray was an innovator. You only need to look at the work she did in her 15 years at the university when it was a research powerhouse. Also of note, she spent time at NU and Harvard so was by no means living in the UC insular bubble that existed in those days among much of the faculty and admin.
O’Neill, on the other hand, is a different story - an entrenched (insulated?) administrator any way you look at it. There is obviously much to like personally, but he was at least part of the problem that Sonnenschein was brought in to fix. The results under O’Neill speak for themselves. He joined College Admissions in 1981 and was appointed Dean in 1989. In that time, and up till his contemporary Michael Behnke was brought in to turn things around within a year, O’Neill presided over a truly mediocre admissions record. Clearly, the College was an awkward subject for decades at the university; this was a LONG standing issue. But O’Neill didn’t help, so he really can’t be seen as more than part of the fossilization that began after Hutchins and continued for quite a spell. However, in all fairness, his personalized style of admissions made him famous among his contemporaries and it is to be hoped that he influenced not only admissions offices everywhere, but - at UChicago - the admissions practices they use today.
Perhaps, Cue, you are happier with “paralyzed” rather than fossilized? I’m cool with either. This is an objective assessment, btw - no one at the university (especially those “cynical, pragmatic and calculated” New-Guard types that you’ve described) is above a critique.
Where is your evidence that the “new guard” just follows along with whatever the trustees decide? Trustees rely heavily on the university’s executive team for advice and for ideas as to how to carry out the vision that they have for the university (including timing). They also hire the pres. Other than give oodles to the university itself, that’s probably their most important job. BTW, Gray, Provost Casper and the trustees were WELL AWARE of the financial crisis. They just didn’t share it all with Sonnenschein because they didn’t want to scare him away 
IMO, there has been plenty of evidence of innovation in the past 20+ years. If “heeding market forces” was all that it took to build the College and the endowment, Cue, what does that say about O’Neill and the “old guard”?
The university’s past is filled with battles between the “purists” and the “bottom-liners.” Sonnenschein was perhaps the most forceful of the latter category. But he was by no means the first one in the university’s history. So you are probably right: “innovator” may not be the best descriptor either.
So how about this: “butt-kicker.” And here is a quick description of the last 90 years: In Hutchins day, the “butt-kicker” was the “purist” and the “paralyzed” were the “bottom-liners.” But that switched after his retirement, and it was “pure and paralyzed” for decades even as more “purist but butt-kicker-wannabee” tpes such as Gray tried to turn it around. Then Sonnenschein, the “bottom-liner” came in and kicked major butt, followed by Randal (who was nicer about it). Now, under Zimmer, I see a good blend of “pure” and “bottom-line” and even some “butt-kicking” where necessary. It’s a nice place to be.