Of course. Terrorism should not be tolerated EVEN if you support the cause it claims to work for.
Neat little morality slogan. Terrorism has been always tolerated provided it was beneficial for the winning side. If we are to look at an example from recent ones, Americans used terrorism to win against Britain in order to become independent and not only it was tolerated the people behind them were branded heroes of war.
Truly nowadays such an act of terrorism is abhorrent, inexcusable and not an effective carrier of change. People react to exercises of strength or violence in a different manner and a non aggressive approach is much more plausible because most of our societies have democratic regimes or even before those at least in the past 3 centuries there was a diffusion of authority because of merchantile strength and the rise of the burgeois against the feudal system. Dragon Age is clearly a feudal society and not a particularly enlightened one politically.
The common people have no electoral power and very minor purchasing power. The feudal lords have very limited electoral power which is under the constant censure of military and religious power centers. Ferelden is perhaps further advanced because its existence is in opposition to Orlais; their nationalism is defined in opposition to Orlesian norms and it is well likely that the Orlesians could reclaim it at any moment. Kirkwall is much different. Its viscounts are presented to have ruled under the approval of the chantry and templars. If the common people rebelled against Meredith, she would simply put them down; in fact Leliana makes it pretty clear that the Divine might well put the entire city to the torch. In this balance, one should consider the choice made by Anders. Against ethnic cleansing and tyranny what Anders did is not any greater evil, in fact it pales in comparison.
Being a solider is not the same as being a clergy member. Meredith is guilty on murdering innocent people in the annulment. But so is Anders. He caused it to happen. If you can say Anders is damaged, Meredith is also suffering from the effects of the idol. If she was a danger to others, then he removed the only thing stopping her from becoming and unhinged and specifically made her angry by killing her friend. It happened because of him. And he intended it for it happen. But I don't consider Meredith to be innocent of her actions. She bears responsibly for the terrible choices she made, and so does Anders. He's a monster and she chose to burn down the world and damn the innocents who burn with it.
Having a cause and being evil are not mutually exclusive. Even if the cause is noble. And I don't even think his is. But what you said was "what he did cannot be classified as evil unless you are biased against mages" but it can. Absolutely 100%.
I pretty much answered this in response to admiral above so I suggest you read this comment. But to add to that: If Anders really knew how Meredith would react then one must consider what the hell is she doing at top of chain of command. She was quite damaged and biased before the idol because of what happened to her sister, she should never have become a Templar in first place. Based on this fact what's stopping other Templars from doing what Meredith did? It wouldn't be the first time whole mages get punished for something they absolutely had nothing to do with. That's precisely what Anders was trying to do. To show the mages they are never safe and are living with templar swords below their throat waiting to be slit at an offense they had nothing to do with. Kirkwall incident was the main motive all mages rebelled. The asunder characters played their part and made votes but it was the very anger at events of Kirkwall and unjust annulment of its circle that drew mages to rebel. Because they realized, clear as day, that they can and they will get punished for something that had absolutely nothing to do with.
So go on ahead and call Anders "evil", but the only thing which is 100% certain is he did that to oppose much greater "evils" such as ethnic cleansing.