Simple, if you help the Templars than you will have greater control of the situation and can possibly save more lives and minimize damage. The Templars also have a deep respect for Hawke if you fight with them and those like Cullen don't approve of the massacre of Mages that refuse to fight. They even choose Hawke, if you tell them to spare Mages that surrender, over Meredith despite the fact that Meredith should have power over the Templars and not you as you hold no position within their order.
Not to mention that helping the Templars could help dissuade a Holy War or calls for a March upon Kirkwall. You also get to rule Kirkwall for a bit so you can set things right since after DAII no one has the amount of political and public support that Hawke has within Kirkwall.
While if you side with the Mages than there no chances open to save surrendering Mages and all of the Mages end up getting slaughtered anyway but the lucky few that get to run for the rest of their lives as hunted apostates! Kirkwall is also reduced to ruins with no one strong enough to lead them as they're divided and no one has the strength or pull that Hawke has within Kirkwall following DAII events.
It's also the duty of the Champion to pursue only the paths that are in best interests of Kirkwall.
The Blood Mage issue had also grown tremendously over the years and Mages are actively summoning Demons within the streets of Kirkwall and committing mass murders. Not to mention that there were those plotting to take power unlawfully, and possibly murder Meredith without putting her on trial, thus making them no better than Meredith in that regard.
Sure, not all Mages are Blood Mages but by the end of DAII a large portion of them had given in to the temptation as many try to kill you with Blood Magic. Only those that didn't succumb to Blood Magic try to surrender to you and you can overule Meredith and have their lives spared. Whether those that did succumb to Blood Magic did so because of Meredith or not is irrelevant, the fact of the matter is that there are masses of angered Blood Mages who're all huge threats to Kirkwall and they had to be put down as they were literally tearing the city apart and doing far more damage than the Templars ever did.
Besides, Orsino could have surrendered. If he and the Mages surrendered without a fight than Meredith would lose support and there's no way the Templars like Cullen would stand for mass executions of Mages who aren't resisting. Meredith insisting it be done anyway would cause Cullen to try and relieve her of her command and it would also give credit to the many rumors that Meredith had gone insane. Than of course Meredith would resist and die to Hawke.
Orsino's hands weren't clean either, he kept reports of Blood Mages and Blood Magic to himself because he cared more about image than what was right. Keeping those secrets only served to cause Meredith to feel that she was right in her actions and fueled her fears that of all the Mages of the circle practiced Blood Magic which was augmented by the idol which she had for years. Not to mention that Orsino encouraged and supported the research of the man who murdered your mother. Had Orsino done his duty than your mother wouldn't have died nor would those other women. Yet once again he chose image over doing the right thing and lives were lost because of him.
Orsino also had strong evidence and even suspicions that quite a few of the Mages in the Circle were practicing Blood Magic and quite a few were sneaking out of the Circle for unknown and suspicious reasons. He chose to keep this to himself because all he cared about was image and he refused to believe that the Circle was tainted from within after all despite the fact that Hawke reports multiple times of encountering said Blood Mages.