Does anyone else always side with Meredith?

Try the TOS of pretty much any forum out there.

I live in a world where we have a basic idea of how people think, and why that way of thinking leads to conflict when people are mistreated for crimes they did not commit. I also live in a world where just because something did happen historically doesn't mean it had to happen. Last but not least, I live in a world where people possess deductive reasoning. If you think that the Circle has modified its policy on keeping mages from their families over the years, then please provide examples of them doing so. Otherwise you are assuming facts not in evidence.

Provocation is exactly what you've done at points with your use of emojis. Thank you for admitting that you were trolling.

It is simple. People and institutions are fallible, yes, but are they willing to change for the better when flaws are found? The Circle has clearly shown that it is not. In fact, the Circle actively resists any sort of improvement even as atrocities continue to pile up, to the point that it is actively doing the opposite of what it was originally created for, which is to protect the mages both from the dangers of magic and from the fear non-mages exhibit. Instead of examining why it is causing the problems it is supposed to prevent, it doubles down on the actions that are causing those problems in the first place, further pushing away the people it claims to protect.

No, there is no indication that Jowan was properly training Connor. Considering Jowan himself was a blood mage, and a rather inept one, I find it unlikely that he knows how to train anyone. He also states that he was brought in to teach Connor how to hide his magic from others, not how to control his magic or to resist the allure of demons. The failure to teach him the latter directly led to the undead catastrophe.

Also, my solution has never involved mage children being surrounded by loved ones during the most vulnerable stage of their training. Maintaining contact yes, provided the family itself hasn't rejected their mage child, but with the Circle/College as more of a boarding school where certain tests, possibly including the Harrowing, need to be passed in order to go out into the world. As I've stated before, only the most die-hard Libertarians think that there should be no enforcement to prevent the abuse of magic at all.

This is the second time that you've claimed that you won't respond anymore. You'll have to excuse me if I don't hold my breath.

I don't blame the Templar Order, but the whole system. The Templars behave like the system wants them to behave. Also: I believe, that a humane system, where the magic isn't a "sin" can handle the problem with a better chance... we saw what happened in the current system. The current system's "problem-solving" was a failure: it was disastrous, undoubtedly: she destroyed the whole neighbourhood. It can not be worse but can be better... The system failed, and yes, despite that the girl was weak, I see the better chance to her in a humane system. I already said why: because the parents would call a mage earlier if they are not afraid of the consequences as well, not just their daughter's feeling.

We can't be sure about anything that not happened, of course, but we can calculate the chances and the outcomes. The fact: we saw the worst scenario: the massacre already happened, and the system was not able to handle. And in the outcome, the inhumane system played a big role.

Not just in that case. In Connor's case as well, and probably were more cases as well.

Disasters can happen in a humane system as well, Of course, can. Disasters always happen. let's see: the Dalish clans don't have Circles, but seems they're fine with magic/mages, just like the Avvars. We heard accidents, disasters caused by a mage, Of course. But more than in the Southern-system? Not. And this is my point. Humane system, with less disastrous event. An absolutely win-win situation.

I think the system is the big part of that disaster what Amelia caused. But even if this would be inevitable (what I don't think), can't justify the system – but strongly against it. The raging abominations are canonically very rare. And I don't see, the system was more effective to prevent the disasters what they can cause, than the other, more humane alternatives – but with the persecution, the system can cause disasters. That was my point.

I don't prefer to separate mages totally during their studies, on the contrary, but a boarding school is a good idea. 

Canonically? Absolutely
My Hawke saw what life was like as an apostate and wants none of it.
Plus siding with the mages as a Mage would mean turning against Carver and Aveline and forcing both to choose between their loyalty to Hawke vs their loyalty to law and order and he couldn’t do it.

Plus in the Templar ending Hawke actually had the option to spare/save a few mages, unlike the Mage ending

Most of the mages that Meredith condemns do not want to be apostates. That is the whole point. Meredith uses the actions of an apostate, Anders, to condemn all the law abiding mages inside the Circle. Even if you support the Circle system, siding with Meredith is not doing this. It is why I always argue that even if Hawke is wholly loyal to the Chantry and the Circle system, even if they supported Meredith at the beginning of Act 3, this should be the point at which they say enough is enough. Even Sebastian agrees with this. As he says, the culprit is standing right there in front of you, Meredith, admitting to the crime so why talk of Annulments? So execute Anders but protect the Circle mages. That is justice and that is abiding by the law. Aveline has never turned against me for doing this even when she was mid range on the friendship/rivalry scale. Also, if you are a mage, then Meredith has just condemned every mage in the city to death, so it should hardly be a surprise when she turns on you at the end.

As for Carver, he made his choice when he joined the Templars. That is when he turned against his sibling. He might say that he won't turn you in but he should have realised that at some point he would have to make the choice between the Order and his apostate sibling. That point is reached when Meredith declares the Annulment. As I say above, that applies to every mage in the city, since apostates are automatically outside the law anyway and all the mages in the Circle are effectively condemned as well. That is what Annulment means. Unlike Sebastian, Carver doesn't even question it. That is the extent of his loyalty to his sibling. So why feel loyalty to him?

Of course, I realise that the writers make it seem purely a choice between whether you support mage freedom or not, which ignores all the other issues involved and limits role playing. Varric's comments on your decision reflect this. So from that perspective, it does seem as though if you support the Circle system you have to opt for Meredith and her illegal annulment.  It is rather disappointing that after all the careful political build up and nuanced approach to the issue, in the end they made it a straight forward choice in this way.