I think you are being a bit subjective here.
More than you? Perish the thought.
The mages Vivienne kills are no less rebellious than sect leaders Leliana kills, one cannot be be justified without the other. Its just that these sects leaders are specifically out to get Leliana while the mages just don't want to be locked up in the circles again. I think the implication is clear. Taking aggression when you are absolutely sure you are going to be targeted is actually a defensive move. You know what they say, best defense is a good...
Hypocrisy?
The mages Vivienne kills are killed after rebelling against sanctioned leader who, by the laws of the recognized legitimate authorities of the land, has the position to make such calls on sanctioned mage gatherings. The political opponents Leliana kills are not in revolt, and no law in the land allows the Chantry to summarily execute dissidents or non-believers (though, considering that Leliana is the one changing doctrine, even that label is suspect).
The thing with Leliana is that all her ideas benefit the common people and the oppressed and these people severely outnumber the privileged and people in power. So she has the benefit of majority in mind. Some corruptions in the Chantry are revealed in DA:I, Leliana fixes them all. The sect leaders who rise against her almost immediately are obviously the sort of people who fed on this corruption, because after Leliana they can no longer have the power and resources they used to.
Lelaiana's reforms, to date, have not uniquely benefited 'the common people' as defined by majoritarian, class, or power dynamics.
The foremost beneficiaries of her reign are the mages- who, on many levels, have sever power imbalances in their favor over all non-mages, while Leliana systemically removes the few proven checks on them that Thedas has ever seen.
The secondary beneficiaries of her reign are the elves... who are not a majority by any means, and were not oppressed by the Chantry. They suffered fromthe local authorities and bigoted persons that the Chantry already wasn't sanctioning in their bigotry and oppression, and their oppressors remain firmly in power. The Cantical is a symbol of oppression- restoring it does not actually change their status in society.
The third beneficiary in her reign are those who were previously restricted from entering the priesthood, which, while restrictive, was far from a common point of contention to the people of Thedas. As the Chantry religious leadership was restricted by gender and race, not class, this will most benefit those already within the Chantry or most able to take advantage of the opportunities... which would be the nobility, who on top of sons (and daughters) already serving in the establishment, have the financial means to have competitive advantage in accessing the new opportunities even as the slots are nominally open to all.
As for comparison of hardened Leliana to Cassandra and Leliana, first of all the comparison cannot be made with at least some hindsight which is never good if the comparison is solely based on judge of character. I'm sure you agree that killing power hungry priests who oppose you because you took away their power is safer than persuading them? Softened Leliana is like Gandhi who will end up assassinated because some fanatics simply cannot be persuaded. Hardened Leliana is like Queen Elizabeth of England who lived a very long life and thanks to her large spy networks and political power transformed England from religious backwater with fat priests to land of art, literature and human advancement. She is usually regarded as most important woman in history of England. Actually the resemblance to Leliana is astonishing because she also killed fanatical religious leaders, removed social class requirement in many professions such as knighthood and got the love of common people and the oppressed. Oh and she had red hair 
We are posters in a forum evaluating a fictional character, not justifying a role-playing decision in the moment. We are absolutely entitled to use hindsight, and side-sight, and even foresight.
Choice of historical comparison aside- if you want to choose a leader who made enduring social changes there are far better, albeit less authoritarian, leaders to choose from- the argument you make to defend Leliana can just as well be used to describe Vivienne. Crushing a rebellion is 'safer' than letting it fester. The merits of concentrating power in an institution built around one's self.
As for circles, Leliana disbands the old circle system. "Circle" is just a name at this point, she gives the freedom to mages to create whatever institution they prefer. They create the college, they could have created another version of Circleif they wanted, like Vivienne does. No one was stopping them, certainly not Leliana. Leliana is the only divine that gives a choice to the mages instead of dictating one for them and they always end up creating the college, which says a lot here.
Indeed- it says that people will always grasp for as much power as they can get away with, which is very concerning when the people in question have a very recent history of being reckless, undisciplined, and outright incompetent while being ambivalent or worse on the well-being of anyone but themselves.
The Mages who want the College most are also the mages who thought Fiona- one of the most disastrous leaders in modern mage history- was a good person to follow. If you thought defending Xil was fun, you're going to love defending Fiona.
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