She undermined the Templars precisely because they weren't willing to compromise. They had their idea of what the Maker's will was and that was whatever they wanted to do. Wynne and the other Aequitarians wanted a compromise, they wanted reform without breaking away from the Chantry. In the end all that Lambert did was push the Aequitarians into the arms of the libertarians in an attempt to escape his tyranny. But the templars who follow the new Divine are those that are rescued or joined the Inquisition willingly, they have the true vision of the templars in mind. They also don't have the Seekers to lead them anymore. Justinia wasn't weak, she just couldn't contend with the extremist elements of the organisation which had become part of every level. She couldn't control them because they had become uncontrollable, fixated on the belief that only they had all the answers. The Seekers may have been happy to serve the Divine for hundreds of years but the moment they felt like they were being coerced into accepting reforms, into aligning with the Divine's wishes, they closed ranks and rebelled.
And what she did with Fiona and Adrian? Those 2 didnt wanted a compromise too, and she did nothing.
Tell me why the templars should accept the compromise? In this "compromise" their side gains nothing and the mages gains everything, this is not a compromise.
If Justinia cant control her own man and need to assassinate them she is weak, the templars recruited at Therinfal were the same who served her. Look at Cassandra she rally the remaing Seekers and they follow her withouth question, because they trust her and she is competent, Justinia couldnt do that.
Her argument falls flat for me since Vivienne herself doesn't have to live in isolation or abide by the same Chantry rules she spouts for other mages.
In fact, she enjoys more freedoms and privileges than most non-mages. She has power, influence, political connections, lives in a palace, is the mistress of a powerful noble, frequents court and parties, and apparently can go wherever she wants without a Templar constantly hovering over her shoulder. For all her talk that mages should stay in Circles, she herself doesn't have to stay confined in a Circle. For all her talk that mages need to be regulated, she herself doesn't have to be regulated every second of every day. For example, we see her use magic to freeze (and possibly kill?) a man for insulting a guest "at my party, in my home." Such behavior would get most other "Circle" mages cracked down on and possibly killed by an ever-vigilant Templars faster than you could blink.
Of course she supports the Circle and Chantry regulations; she doesn't have to live there or deal with them.
Vivienne didnt always have her privilegies, she was a normal Circle mage, every freedom she has its because she showed herself trustworth.
And she was the First Enchanter of Montsimmard, if she didnt live in the Circle she couldnt do her job (but ofc she could leave wherever she wanted). If made Divine she gives every mage the same opportunity she had, so why she dont believe in what she says?