The CRA is neither greedy, nor mean or benevolent. They are a government entity operating within a set of policies and specific rules. In almost every guide or set of laws there can be grey areas JT is caught in one of those currently.
As a retired CRA collections officer, I can tell you greed is something that doesnt drive tax collection. I cannot tell you how many times I heard something to the effect of "c'mon just this once, who's going to know." Well for starters at the very least two of us, one of which, me, could be fired and charged with abetting tax evasion by counsel if I went along with that kind of scheme!
I'm sure that John's legal counsel may have thought he found a loop hole all those years ago in his interpretation of how the law is written, and now how JT finds himself in this mess.
If the court finds that he did evade, JT would have to pay the shortfall, the interest accrued and possibly a fine. Not to mention his attorneys fees and court costs.