I'd say that there isn't enough canon evidence to definitively say either way.
Both Medron Pryde AND Stormfury have very valid points.
Yes, the majority of higher command positions were replaced, and most likely stacked with, if not direct Shraplen supporters/allies, then Officers aligned with his political faction. (Nothing too overtly unusual about this, pretty much any serving head of state is going to do the same thing)
Also, Yes, it was a fairly good chunk of time, and since the Officers in question were Regimental commanders and higher at the previous point, they can be assumed to have been fairly senior men and women, with at LEAST twenty years service behind them. A good number of them retiring sheerly out of time in service issues would not be unusual, or any solid indicator of a conspiracy.
Did the TDF commit atrocities?...yes. We can argue until the cows come home about why, but the fact remains that they did. Personally, and speaking purely for myself, my feeling is that a combination of factors played into it. One: essentially Decades of anti-Davion propaganda at all levels of Taurian Society. Two, a predisposition towards suspicion of the Inner Sphere Powers, and Davion in particular. Three, a command staff stacked with members of the Returner faction. And four, outside powers (Word of Blake) meddling in things by stoking the above factors and possibly playing with communications.
Is it POSSIBLE that there was a conspiracy? Yes
Is there sufficient canon "Proof"? unfortunately No.
But then again, a properly executed conspiracy is VERY hard to prove. Done right, every move will be easily explainable and justifiable on its own. None of the individual moves would, or should, elicit suspicion. That's really the whole POINT of a secret conspiracy, not getting caught.
Of course, this is also Battletech. Conspiracies and secret cabals plotting mischief behind the scenes might not be a certainty, but they are also a fairly safe bet. Proving it now...there's the rub.