There are reasonable criteria for suggesting that Magic should have its own Stack Exchange — such as a desire to attract a community of Magic-focused players who don't identify with the "board games" label — but, from the perspective of this site, its presence isn't a problem.
Here's my argument for why that's the case:
1. Magic isn't drowning out the other content.
For example, I've got Magic as a favorite tag, so here's the front page for me right now:
That's about a third of the content. Someone who's not a fan of the game might grumble a little, but if they block the tag they'll easily be able to browse the site and see questions they're more interested in.
In contrast, over on RPG Stack Exchange, I've got tags related to D&D/D20 (D&D3.5, Pathfinder, D20 system, D&D4, D&D5) on my ignore list, and here's where that gets me:
This is what actually dominating the content looks like.
So why doesn't D&D have its own Stack Exchange, then? Well, that brings us to our next point...
2. In the view of this site, Magic is a part of the broader "board games" ecosystem and community.
A lot of the board-game questions are about what you could call "designer board games" or "hobby board games" — board games that appeal to fairly dedicated players, who enjoy them as a hobby above and beyond the average person's exposure to board games. Many people in that community have played Magic, whether casually or devotedly. Many hobby board game shops are only able to survive because they sell Magic products and run Magic events to get people into the stores.
There's some tradeoffs there: some folks will argue that you could build a bigger or better community if you focused on Magic players who think of themselves exclusively as Magic players. But this site does clearly demonstrate that "board-games" people are happy to ask and answer Magic questions.
And that overlap means that...
3. Magic questions help us get answers to other questions.
By its nature, B&CG isn't a site that attracts a lot of "generic" questions. (There are some: about how to design games, about customizing game components such as miniatures, about structuring board game tournaments.)
It's actually really, really helpful to have a popular game or two that create a constant trickle of questions. Because it means a significant portion of the "expert" user base has something to do on the site every week. This keeps them coming back so they're around when questions about other areas of expertise arise.
Like, imagine you have a user who's really knowledgeable about Magic, Carcassone, Netrunner, and historical recreations of ancient board games. Having that user regularly visit to answer, vote on, or just skim the Magic questions means their eyes are there when questions about the rarer topics come up.
It's similar to how Java and C++ constitute a huge volume of Stackoverflow questions, but splitting either into its own site would hurt Stackoverflow because the people answering Java or C++ questions are also there answering questions about more specialized or esoteric topics. Just like lots of experienced programmers know and care about Java and C++, lots of experienced board-games players know and care about Magic.
Note that I'm not addressing the perspective of a different site. I'm sure there are arguments for why a unique Magic site might be great for that site and its prospective community (you can read them on Area 51, probably). But the key question here is "Is Magic bringing B&CG SE down?" And the answer is, "You can rest easy, because it's actually lifting it up!"